PulmonDB - COVID19.
Regulons Selection: cell lines
Monica Padilla
2022-10-19
## Load functions
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Selection of Regulons based on Differentially Activation and Specificity
Use of Regulon Specificity Scores (also referred here as enrichment although it is not exactly) + Differential Activation (DA) of Regulons Analysis. This is an exploratory report on the parameters used to select regulons. Main code for Regulons Selection = reticulateEnrich.R
DA tests pvalues distributions
Mann Whitney U Test
P-values distributions resulting from Mann Whitney U Test for Differential Activation of Regulons (measured from AUC scores per regulon, Regulon Activity Matrix). Non-adjusted p-values are displayed.
Run reticulateEnrich_.R first.
library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange
pvalues <- as.data.frame(read_csv(paste0(params$inputdir,params$pval_mwu.fn), col_names = T))
# rename cols for display in graphs
if(params$celllines==1){
names(pvalues) <- str_replace(names(pvalues), "SARS-CoV-2", "SARSCoV2")
names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pre-treatment", "pt")
}
plots <- vector('list', length(pvalues)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues)) {
exp <- colnames(pvalues)[i]
print(exp)
plots[[i]] <- ggplot(pvalues,aes(x=.data[[exp]])) + #<<
geom_bar(fill="#9966bb") + # geom hist didnt work
scale_x_binned() +
labs(title = exp, x="pvalue", y="")
}## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu-3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"names(plots) <- names(pvalues)
# display plots together
p <- ggarrange(plots[[1]],plots[[2]],plots[[3]],plots[[4]],plots[[5]], plots[[6]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("P-values Mann Whitney U Tests",face = "bold", size = 14))
## save to png
png(paste0(params$outdir,"hist_pvalues-mwu_01.png"), width = 600, height = 600)
p
dev.off()## png
## 2p <- ggarrange(plots[[8]],plots[[7]],plots[[9]],plots[[10]],plots[[11]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("P-values Mann Whitney U Tests",face = "bold", size = 14))
png(paste0(params$outdir,"hist_pvalues-mwu_02.png"))
p
dev.off()## png
## 2# minimum p values per experiment
apply(pvalues,2,min)## HPIV3_infected_A549 IAV_infected_A549
## 0.0001770350 0.0003325123
## IAV_infected_NHBE IAVdNS1_infected_NHBE
## 0.0031276088 0.0031276088
## RSV_infected_A549 SARSCoV2_infected_A549
## 0.0002334267 0.0000737137
## SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt
## 0.0021645022 0.0091157873
## SARSCoV2_infected_Calu-3 SARSCoV2_infected_NHBE
## 0.0636025696 0.0050437189
## human_IFNB_treated_NHBE
## 0.0011655012Each pvalue corresponds to a TF/regulon being differentially active in a given experiment vs its control (not shown).
pvalues from TRUE null hypothesis (corresponding to Error Type II) distribution –> uniform distribution in range [0,1]
pvalues from FALSE null hypothesis distribution –> asymetric, skewed to zero
Most of these distributions show that pvalues are more skewed to zero than what we would expect from a uniform distribution thus indicating that most of them correspond to FALSE null hypothesis.
Using a too low significance level would lead to rejecting true positives.[1]
However, the exception is the case of SARS-CoV-2 infected A549 expressing hACE2, where the pvalues distribution is flattened, with a skew towards 1. A strict significance level should be used in this case.
Kolmogrov Test
P-values distributions resulting from Kolmogrov Test for Differential Activation of Regulons (measured from AUC scores per regulon, Regulon Activity Matrix). Non-adjusted p-values are displayed.
library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange
pvalues2 <- as.data.frame(read_csv(paste0(params$inputdir,params$pval_klm.fn), col_names = T))
# rename cols for display in graphs
names(pvalues2) <- names(pvalues)
plots2 <- vector('list', length(pvalues2)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues2)) {
exp <- colnames(pvalues2)[i]
print(exp)
plots2[[i]] <- ggplot(pvalues2,aes(x=.data[[exp]])) + #<<
geom_bar(fill="#9966bb") + # geom hist didnt work
scale_x_binned() +
labs(title = exp, x="pvalue", y="")
}## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu-3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"names(plots2) <- names(pvalues2)
# display plots together
p <- ggarrange(plots2[[1]],plots2[[2]],plots2[[3]],plots2[[4]],plots2[[5]], plots2[[6]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("P-values Kolmogrov Tests ",face = "bold", size = 14))
png(paste0(params$outdir,"hist_pvalues-klm_01.png"), width = 600, height = 600)
p
dev.off()## png
## 2p <- ggarrange(plots2[[8]],plots2[[7]],plots2[[9]],plots2[[10]],plots2[[11]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("P-values Kolmogrov Tests",face = "bold", size = 14))
png(paste0(params$outdir,"hist_pvalues-klm_02.png"), width = 600, height = 600)
p
dev.off()## png
## 2apply(pvalues,2,min)## HPIV3_infected_A549 IAV_infected_A549
## 0.0001770350 0.0003325123
## IAV_infected_NHBE IAVdNS1_infected_NHBE
## 0.0031276088 0.0031276088
## RSV_infected_A549 SARSCoV2_infected_A549
## 0.0002334267 0.0000737137
## SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt
## 0.0021645022 0.0091157873
## SARSCoV2_infected_Calu-3 SARSCoV2_infected_NHBE
## 0.0636025696 0.0050437189
## human_IFNB_treated_NHBE
## 0.0011655012DA tests adjusted pvalues distributions
Mann Whitney U Test
Get dataframes of adjusted pvalues from both test to work with locally:
# on the cluster
# Run `reticulateEnrich_.R` first
library(tidyverse)
# retrieve adjusted pvalues from difregs script
pvalues_adj <- py$pvalues_adjusted
pvalues_adj2 <- py$pvalues_adjusted2
# turn to dataframes
pv.adj.mwu <- t(data.frame(matrix(unlist(pvalues_adj), nrow=length(pvalues_adj), byrow=TRUE)))
colnames(pv.adj.mwu) <- keys_ct
pv.adj.klm <- t(data.frame(matrix(unlist(pvalues_adj2), nrow=length(pvalues_adj2), byrow=TRUE)))
colnames(pv.adj.klm) <- keys_ct
if(celllines==1){
colnames(pv.adj.mwu) <- str_replace_all(colnames(pv.adj.mwu), "-", "")
colnames(pv.adj.mwu) <- str_replace(colnames(pv.adj.mwu), "w_vector_expressing_", "")
colnames(pv.adj.mwu) <- str_replace(colnames(pv.adj.mwu), "1hr_Ruxolitinib_pretreatment", "pt")
colnames(pv.adj.klm) <- colnames(pv.adj.mwu)
}
write.csv(pv.adj.mwu, file = paste0(outdir,"pvalues-mwu-2t-adjusted.csv"), quote = F, row.names = F)
write.csv(pv.adj.mwu, file = paste0(outdir,"pvalues-klm-2t-adjusted.csv"), quote = F, row.names = F)Make plots:
library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange
pv.adj.mwu <- as.data.frame(
read_csv(file = paste0(params$inputdir,params$adj_pvals_mwu.fn),col_names = T))## Rows: 898 Columns: 11
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (11): HPIV3_infected_A549, IAV_infected_A549, IAV_infected_NHBE, IAVdNS1...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.pvalues <- pv.adj.mwu # just changed this #<<
# rename cols for display in graphs
if(params$celllines==1){
names(pvalues) <- str_replace(names(pvalues), "SARS-CoV-2", "SARSCoV2")
names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pre-treatment", "pt")
}
plots <- vector('list', length(pvalues)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues)) {
exp <- colnames(pvalues)[i]
print(exp)
plots[[i]] <- ggplot(pvalues,aes(x=.data[[exp]])) + #<<
geom_bar(fill="#9966bb") + # geom hist didnt work
scale_x_binned() +
labs(title = exp, x="pvalue", y="")
}## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"names(plots) <- names(pvalues)
# display plots together
p <- ggarrange(plots[[1]],plots[[2]],plots[[3]],plots[[4]],plots[[5]], plots[[6]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("Adjusted P-values Mann Whitney U Tests",
face = "bold", size = 14)) # and this
png(paste0(params$outdir,"hist_adj-pvalues-mwu_01.png"), width = 600, height = 600)
p
dev.off()## png
## 2p <- ggarrange(plots[[8]],plots[[7]],plots[[9]],plots[[10]],plots[[11]],
ncol = 2, nrow = 3)
annotate_figure(p,top = text_grob("Adjusted P-values Mann Whitney U Tests",face = "bold", size = 14)) # and this
png(paste0(params$outdir,"hist_pvalues-mwu_02.png"), width = 600, height = 600)
p
dev.off()## png
## 2# minimum p values per experiment
apply(pvalues,2,min)## HPIV3_infected_A549 IAV_infected_A549
## 0.039744348 0.021328286
## IAV_infected_NHBE IAVdNS1_infected_NHBE
## 0.024405490 0.024965249
## RSV_infected_A549 SARSCoV2_infected_A549
## 0.016124398 0.002364104
## SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt
## 0.080988456 0.130623943
## SARSCoV2_infected_Calu3 SARSCoV2_infected_NHBE
## 0.237566138 0.106146572
## human_IFNB_treated_NHBE
## 0.037379287Kolmogrov Test
library(tidyverse) ## gplot, dplyr, stringr
library(ggpubr) ## ggarange
pv.adj.klm <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_klm.fn), col_names = T))
pvalues2 <- pv.adj.klm # just changed this #<<
# rename cols for display in graphs
names(pvalues2) <- names(pvalues)
plots2 <- vector('list', length(pvalues2)) # list of plots
# create plots iteratively
for (i in 1:ncol(pvalues2)) {
exp <- colnames(pvalues2)[i]
print(exp)
plots2[[i]] <- ggplot(pvalues2,aes(x=.data[[exp]])) + #<<
geom_bar(fill="#9966bb") + # geom hist didnt work
scale_x_binned() +
labs(title = exp, x="pvalue", y="")
}## [1] "HPIV3_infected_A549"
## [1] "IAV_infected_A549"
## [1] "IAV_infected_NHBE"
## [1] "IAVdNS1_infected_NHBE"
## [1] "RSV_infected_A549"
## [1] "SARSCoV2_infected_A549"
## [1] "SARSCoV2_infected_A549_hACE2"
## [1] "SARSCoV2_infected_A549_hACE2_pt"
## [1] "SARSCoV2_infected_Calu3"
## [1] "SARSCoV2_infected_NHBE"
## [1] "human_IFNB_treated_NHBE"names(plots2) <- names(pvalues2)
# display plots together
p <- ggarrange(plots2[[1]],plots2[[2]],plots2[[3]],plots2[[4]],plots2[[5]], plots2[[6]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("Adjusted P-values Kolmogrov Tests",
face = "bold", size = 14)) # and this
png(paste0(params$outdir,"hist_adj-pvalues-klm_01.png"), width = 600, height = 600)
p
dev.off()## png
## 2p <- ggarrange(plots2[[8]],plots2[[7]],plots2[[9]],plots2[[10]],plots2[[11]],
ncol = 2, nrow = 3)
# add title
annotate_figure(p,
top = text_grob("Adjusted P-values Kolmogrov Tests",
face = "bold", size = 14)) # and this
png(paste0(params$outdir,"hist_adj-pvalues-klm_02.png"), width = 600, height = 600)
p
dev.off()## png
## 2apply(pvalues,2,min)## HPIV3_infected_A549 IAV_infected_A549
## 0.039744348 0.021328286
## IAV_infected_NHBE IAVdNS1_infected_NHBE
## 0.024405490 0.024965249
## RSV_infected_A549 SARSCoV2_infected_A549
## 0.016124398 0.002364104
## SARSCoV2_infected_A549_hACE2 SARSCoV2_infected_A549_hACE2_pt
## 0.080988456 0.130623943
## SARSCoV2_infected_Calu3 SARSCoV2_infected_NHBE
## 0.237566138 0.106146572
## human_IFNB_treated_NHBE
## 0.037379287FDR threshold on adjusted p-values
Mann Whitney U Test
Import dataset and call source script with functions:
library(tidyverse)
## call functios
source("~/Documents/RegGenoLab/COVID19/PulmonDB_COVID/COVID/bulk/rScripts/FDRthreshold_functions.R")
## dataset
pv.adj.mwu <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_mwu.fn), col_names = T))
pv.adj.mwu <- as.data.frame(pv.adj.mwu)
# rename cols for display in graphs
if(params$celllines==1){
names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "SARS-CoV-2", "SARSCoV2")
names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "w_vector_expressing_", "")
names(pv.adj.mwu) <- str_replace(names(pv.adj.mwu), "1hr_Ruxolitinib_pre-treatment", "pt")
}
#head(pv.adj.mwu)thrs.mwu <- regsPerFDRthr(pv.adj.mwu, fdr_lowth = 0.1, fdr_upthr = 0.24)
thrs.mwuSe buscó que el FDR threshold (entre 0.2 y 0.1) elegido permitiera que nos quedaramos con alrededor de 100 regulones por experimento. Esto puesto que el set de regulones se someterá a otros filtros: - pvalor ajustado en test de Kolmogrov - LFC de enriquecimiento de regulon en el experimento dado En conjunto, estos filtros darán lugar a un set de regulones cuya especificidad y relevancia en el experimento dado sean relativamente confiables.
El FDR threshold elegido por experimento se especifica aquÃ:
fdrs.mwu <- getChosenFDRth(thrs.mwu, min.regs = c(100,30))
fdrs.mwuKolmogrov Test
thrs.klm <- regsPerFDRthr(pv.adj.klm, fdr_lowth = 0.1, fdr_upthr = 0.24)
thrs.klmEl FDR threshold elegido por experimento se especifica aquÃ:
fdrs.klm <- getChosenFDRth(thrs.klm, min.regs = c(100,30))
fdrs.klmRegulons Counts After Filtering
DA:
After taking common Differentialy Activated Regulons from both tests:
tfs_da.fn <- paste0(params$inputdir, params$tfs_DA_2t.fn)
tfs_da <- readRDS(tfs_da.fn)
# at reticulateEnrich line 117
## check how many regulons were kept
t(as.data.frame(lapply(tfs_da,length)))## [,1]
## HPIV3_infected_A549 123
## IAV_infected_A549 243
## IAV_infected_NHBE 287
## IAVdNS1_infected_NHBE 287
## RSV_infected_A549 47
## SARSCoV2_infected_A549 222
## SARSCoV2_infected_A549_hACE2 29
## SARSCoV2_infected_A549_hACE2_pt 184
## SARSCoV2_infected_Calu3 378
## SARSCoV2_infected_NHBE 141
## human_IFNB_treated_NHBE 31✅ Filter Applied
Differentiate between Up and Down Regulated regulons based on logFC (infection/mock):
library(tidyverse)
## Load Data
# auc_mtx
auc_mtx <- readRDS(paste0(params$inputdir,params$auc_mtx))
# Load data: TFs names (in order after just scenic counts cutoff)
tfs <- as.data.frame(read_csv(paste0(params$inputdir,params$tfs.fn), col_names = F))[,1]## Rows: 898 Columns: 1
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): X1
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.tfs <- stringr::str_remove(tfs, "_\\(\\+\\)")
tfs <- tfs[match(str_remove(colnames(auc_mtx),"_\\(\\+\\)"), tfs)]
# Load and tidy data: log 2 FC (auc_mtx)
l2fc <- as.data.frame(read_csv(paste0(params$inputdir,params$l2fc.fn), col_names = T))## Rows: 898 Columns: 11
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (11): HPIV3_infected_A549, IAV_infected_A549, IAV_infected_NHBE, IAVdNS1...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.if(params$celllines==1){
names(l2fc) <- str_replace_all(names(l2fc), "-", "")
names(l2fc) <- str_replace(names(l2fc), "w_vector_expressing_", "")
names(l2fc) <- str_replace(names(l2fc), "1hr_Ruxolitinib_pretreatment", "pt")
}
rownames(l2fc) <- colnames(auc_mtx)
head(l2fc)## match dfs rows (tfs)
l2fc <- l2fc[match(str_replace(tfs,"$","_\\(\\+\\)"),rownames(l2fc)),]
## Make lists of up/down regulons
tfs_da_up = list()
tfs_da_down = list()
for (exp in names(tfs_da)) {
tfs_da_up[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc)[which(l2fc[exp] > 0)]]
tfs_da_down[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc)[which(l2fc[exp] < 0)]]
}
# make df of counts of regulons
n_up <- t(as.data.frame(lapply(tfs_da_up,length)))[,1]
n_down <- t(as.data.frame(lapply(tfs_da_down,length)))[,1]
data.frame(up = n_up, down = n_down)✅ Filter Applied for Upregulated Regulons
DA + specificity:
After filtering regulons for those that had an optimal LFC enrichment :
tfs_da_enrich.fn <- paste0(params$inputdir, params$tfs_DA_enrichLFC_2t.fn)
tfs_da_enrich <- readRDS(tfs_da_enrich.fn)
names(tfs_da_enrich) <- names(tfs_da)
# at reticulateEnrich line 117
## check how many regulons were kept
t(as.data.frame(lapply(tfs_da_enrich,length)))## [,1]
## HPIV3_infected_A549 2
## IAV_infected_A549 1
## IAV_infected_NHBE 75
## IAVdNS1_infected_NHBE 123
## RSV_infected_A549 0
## SARSCoV2_infected_A549 9
## SARSCoV2_infected_A549_hACE2 17
## SARSCoV2_infected_A549_hACE2_pt 13
## SARSCoV2_infected_Calu3 202
## SARSCoV2_infected_NHBE 7
## human_IFNB_treated_NHBE 24
Differentiate between Up and Down Regulated regulons again:
## Make lists of up/down regulons
tfs_da_enrich_up = list()
tfs_da_enrich_down = list()
for (exp in names(tfs_da_enrich)) {
tfs_da_enrich_up[[exp]] <-
tfs_da_enrich[[exp]][tfs_da_enrich[[exp]] %in% rownames(l2fc)[which(l2fc[exp] > 0)]]
tfs_da_enrich_down[[exp]] <-
tfs_da_enrich[[exp]][tfs_da_enrich[[exp]] %in% rownames(l2fc)[which(l2fc[exp] < 0)]]
}
# make df of counts of regulons
n_up <- t(as.data.frame(lapply(tfs_da_enrich_up,length)))[,1]
n_down <- t(as.data.frame(lapply(tfs_da_enrich_down,length)))[,1]
data.frame(up = n_up, down = n_down)For regulons that were Upregulated and enriched, this filter keeps a decent number of regulons, but that’s not the case for Downregulated regulons.
✅ Filter Applied for Upregulated Regulons
Volcano Plots
library(ggplot2)
library(ggrepel)
############################################
## Plots 2t - 2 tails test
# Load and tidy data: regulons/tfs that were in DA + enriched
paste0("using set of DA regulons (tfs): ",tfs_da.fn)## [1] "using set of DA regulons (tfs): ../regulons-analysis/out/celllines/tfs_mwu_ks_fdr1-24-2t.RData"tfs_da.fn <- paste0(params$inputdir, params$tfs_DA_2t.fn)
tfs_da <- readRDS(tfs_da.fn)
if(params$celllines==1){
names(tfs_da) <- str_replace_all(names(tfs_da), "-", "")
names(tfs_da) <- str_replace(names(tfs_da), "_w_vector_expressing", "")
names(tfs_da) <- str_replace(names(tfs_da), "1hr_Ruxolitinib_pretreatment", "pt")
}
tfs_da## $HPIV3_infected_A549
## [1] "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNTL_(+)" "ATF1_(+)"
## [6] "ATF4_(+)" "ATF5_(+)" "BCL6B_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [11] "BRF1_(+)" "CDX1_(+)" "CHD2_(+)" "CLOCK_(+)" "CPEB1_(+)"
## [16] "CREB1_(+)" "CREB5_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F1_(+)"
## [21] "E4F1_(+)" "ELF2_(+)" "ESRRA_(+)" "FOSL1_(+)" "FOXA2_(+)"
## [26] "FOXB1_(+)" "FOXC2_(+)" "FOXF2_(+)" "FOXK1_(+)" "FOXO1_(+)"
## [31] "FOXO3_(+)" "FOXP2_(+)" "GABPB1_(+)" "GCM1_(+)" "HAND1_(+)"
## [36] "HES6_(+)" "HEY1_(+)" "HEY2_(+)" "HIVEP2_(+)" "HLF_(+)"
## [41] "HOXA9_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [46] "HOXC10_(+)" "HOXC13_(+)" "HOXC8_(+)" "HOXD11_(+)" "HSF2_(+)"
## [51] "IKZF2_(+)" "IRF4_(+)" "ISL2_(+)" "KDM5A_(+)" "KLF3_(+)"
## [56] "KLF7_(+)" "KLF9_(+)" "LHX4_(+)" "MAF_(+)" "MAZ_(+)"
## [61] "MECOM_(+)" "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)"
## [66] "NEUROD1_(+)" "NFE2L1_(+)" "NFIA_(+)" "NFIL3_(+)" "NFKB1_(+)"
## [71] "NFKB2_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)" "NKX3-1_(+)"
## [76] "NR2C1_(+)" "NR5A2_(+)" "OTP_(+)" "PAX7_(+)" "POU3F2_(+)"
## [81] "POU5F1_(+)" "RARB_(+)" "RFX2_(+)" "RFX3_(+)" "RREB1_(+)"
## [86] "RUNX2_(+)" "SNAI3_(+)" "SOX1_(+)" "SOX15_(+)" "SP6_(+)"
## [91] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBX15_(+)" "TBX20_(+)"
## [96] "TCF3_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)" "VSX1_(+)"
## [101] "ZBTB33_(+)" "ZBTB7A_(+)" "ZEB1_(+)" "ZFX_(+)" "ZIC2_(+)"
## [106] "ZNF134_(+)" "ZNF143_(+)" "ZNF148_(+)" "ZNF160_(+)" "ZNF227_(+)"
## [111] "ZNF354C_(+)" "ZNF429_(+)" "ZNF449_(+)" "ZNF502_(+)" "ZNF524_(+)"
## [116] "ZNF571_(+)" "ZNF597_(+)" "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [121] "ZNF787_(+)" "ZNF841_(+)" "ZSCAN26_(+)"
##
## $IAV_infected_A549
## [1] "ALX1_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)" "ARNTL2_(+)"
## [6] "ASCL2_(+)" "ATF2_(+)" "ATF4_(+)" "BACH1_(+)" "BATF_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHE40_(+)"
## [16] "BRF1_(+)" "CDX2_(+)" "CLOCK_(+)" "CPEB1_(+)" "CREB5_(+)"
## [21] "CTCFL_(+)" "DLX3_(+)" "DLX5_(+)" "E2F1_(+)" "E2F2_(+)"
## [26] "E2F4_(+)" "E2F5_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)"
## [31] "EGR3_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELF5_(+)"
## [36] "ELK3_(+)" "ELK4_(+)" "EN1_(+)" "EN2_(+)" "ERF_(+)"
## [41] "ESRRA_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)" "ETV7_(+)"
## [46] "FOSB_(+)" "FOSL2_(+)" "FOXB1_(+)" "FOXC1_(+)" "FOXD3_(+)"
## [51] "FOXF2_(+)" "FOXM1_(+)" "FOXO1_(+)" "GABPA_(+)" "GABPB1_(+)"
## [56] "GATA5_(+)" "GCM1_(+)" "GLI1_(+)" "GLIS2_(+)" "GRHL1_(+)"
## [61] "GRHL3_(+)" "GRHPR_(+)" "GSC_(+)" "GSX2_(+)" "GTF2B_(+)"
## [66] "GTF2IRD1_(+)" "HES1_(+)" "HES5_(+)" "HES6_(+)" "HIC1_(+)"
## [71] "HINFP_(+)" "HIVEP2_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [76] "HOXA1_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA6_(+)" "HOXA7_(+)"
## [81] "HOXA9_(+)" "HOXB13_(+)" "HOXB5_(+)" "HOXB7_(+)" "HOXB8_(+)"
## [86] "HOXC10_(+)" "HOXC11_(+)" "HOXC13_(+)" "HOXC5_(+)" "HOXC6_(+)"
## [91] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HTATIP2_(+)" "IRF1_(+)"
## [96] "IRF2_(+)" "IRF3_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)"
## [101] "IRF9_(+)" "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "IRX5_(+)"
## [106] "JUND_(+)" "KLF10_(+)" "KLF3_(+)" "KLF4_(+)" "KLF5_(+)"
## [111] "KLF6_(+)" "KLF8_(+)" "KLF9_(+)" "LBX2_(+)" "LHX2_(+)"
## [116] "LHX5_(+)" "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)" "MAFG_(+)"
## [121] "MAX_(+)" "MAZ_(+)" "MECOM_(+)" "MEOX1_(+)" "MNX1_(+)"
## [126] "MSX2_(+)" "MTF1_(+)" "MXD1_(+)" "MXD3_(+)" "MXD4_(+)"
## [131] "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)" "MYPOP_(+)" "MZF1_(+)"
## [136] "NEUROD1_(+)" "NFATC4_(+)" "NFE2_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [141] "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)" "NKX2-1_(+)"
## [146] "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [151] "NR2F6_(+)" "ONECUT2_(+)" "OTP_(+)" "OTX1_(+)" "OVOL2_(+)"
## [156] "PAX7_(+)" "PAX9_(+)" "PHF21A_(+)" "PHF8_(+)" "PKNOX1_(+)"
## [161] "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F1_(+)"
## [166] "POU2F3_(+)" "POU3F1_(+)" "POU3F4_(+)" "PPARD_(+)" "PRDM1_(+)"
## [171] "PRDM15_(+)" "PRRX2_(+)" "PSMD12_(+)" "RAB18_(+)" "RARG_(+)"
## [176] "REL_(+)" "RFX2_(+)" "RORA_(+)" "RREB1_(+)" "RXRG_(+)"
## [181] "SATB1_(+)" "SETDB1_(+)" "SIN3A_(+)" "SIX2_(+)" "SIX5_(+)"
## [186] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)" "SNAI2_(+)" "SNAI3_(+)"
## [191] "SOX5_(+)" "SP3_(+)" "SP5_(+)" "STAT1_(+)" "STAT2_(+)"
## [196] "STAT5A_(+)" "STAT5B_(+)" "TAGLN2_(+)" "TBPL2_(+)" "TCF12_(+)"
## [201] "TCF3_(+)" "TCF7_(+)" "TEAD4_(+)" "TEF_(+)" "TFAP2A_(+)"
## [206] "TFAP2C_(+)" "TFAP2E_(+)" "TFDP2_(+)" "TGIF2_(+)" "TLX2_(+)"
## [211] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VDR_(+)"
## [216] "VSX2_(+)" "ZBTB7A_(+)" "ZFX_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [221] "ZNF208_(+)" "ZNF219_(+)" "ZNF274_(+)" "ZNF281_(+)" "ZNF35_(+)"
## [226] "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)" "ZNF483_(+)"
## [231] "ZNF502_(+)" "ZNF524_(+)" "ZNF554_(+)" "ZNF560_(+)" "ZNF597_(+)"
## [236] "ZNF672_(+)" "ZNF682_(+)" "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)"
## [241] "ZNF761_(+)" "ZNF773_(+)" "ZNF787_(+)"
##
## $IAV_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)"
## [4] "ALX3_(+)" "ALX4_(+)" "AR_(+)"
## [7] "ARID5B_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [10] "ATF1_(+)" "ATF3_(+)" "BACH2_(+)"
## [13] "BATF_(+)" "BCL3_(+)" "BCLAF1_(+)"
## [16] "BDP1_(+)" "BHLHE41_(+)" "BNC2_(+)"
## [19] "BORCS8-MEF2B_(+)" "BRF1_(+)" "CCNT2_(+)"
## [22] "CDX2_(+)" "CEBPA_(+)" "CEBPB_(+)"
## [25] "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)"
## [28] "CKMT1B_(+)" "CLOCK_(+)" "CNOT3_(+)"
## [31] "CPEB1_(+)" "CPSF4_(+)" "CREB1_(+)"
## [34] "CREB3_(+)" "CREB3L1_(+)" "CUX1_(+)"
## [37] "DBX1_(+)" "DLX2_(+)" "DLX4_(+)"
## [40] "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [43] "E2F3_(+)" "E2F4_(+)" "E2F6_(+)"
## [46] "EGR1_(+)" "EGR2_(+)" "EGR3_(+)"
## [49] "ELK3_(+)" "EMX1_(+)" "EN1_(+)"
## [52] "EN2_(+)" "ENO1_(+)" "EP300_(+)"
## [55] "ERF_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [58] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)"
## [61] "EVX2_(+)" "FGF19_(+)" "FOS_(+)"
## [64] "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)"
## [67] "FOXB1_(+)" "FOXC1_(+)" "FOXC2_(+)"
## [70] "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [73] "FOXD4L6_(+)" "FOXF2_(+)" "FOXJ2_(+)"
## [76] "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [79] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [82] "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [85] "GCM1_(+)" "GLIS2_(+)" "GMEB1_(+)"
## [88] "GRHL2_(+)" "GTF2IRD1_(+)" "HAND1_(+)"
## [91] "HDAC1_(+)" "HES5_(+)" "HEY1_(+)"
## [94] "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [97] "HNF1A_(+)" "HNF1B_(+)" "HOXA10_(+)"
## [100] "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [103] "HOXB13_(+)" "HOXB4_(+)" "HOXB6_(+)"
## [106] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [109] "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)"
## [112] "HOXC8_(+)" "HOXC9_(+)" "HOXD11_(+)"
## [115] "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [118] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [121] "IKZF3_(+)" "ING3_(+)" "IRF1_(+)"
## [124] "IRF4_(+)" "IRX2_(+)" "IRX5_(+)"
## [127] "ISL2_(+)" "JUN_(+)" "JUNB_(+)"
## [130] "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [133] "KLF10_(+)" "KLF11_(+)" "KLF12_(+)"
## [136] "KLF13_(+)" "KLF14_(+)" "KLF2_(+)"
## [139] "KLF5_(+)" "KLF8_(+)" "LHX4_(+)"
## [142] "LHX8_(+)" "LHX9_(+)" "LMX1B_(+)"
## [145] "MAF_(+)" "MAFB_(+)" "MAFF_(+)"
## [148] "MAFG_(+)" "MEF2B_(+)" "MEF2C_(+)"
## [151] "MEOX2_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [154] "MNT_(+)" "MNX1_(+)" "MSX1_(+)"
## [157] "MSX2_(+)" "MYEF2_(+)" "MYOD1_(+)"
## [160] "MZF1_(+)" "NFATC2_(+)" "NFE2L2_(+)"
## [163] "NFE2L3_(+)" "NFIA_(+)" "NFIB_(+)"
## [166] "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)"
## [169] "NHLH1_(+)" "NKX2-1_(+)" "NKX2-5_(+)"
## [172] "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [175] "NR1D1_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [178] "NR3C1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [181] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)"
## [184] "ONECUT2_(+)" "ONECUT3_(+)" "OTP_(+)"
## [187] "PATZ1_(+)" "PAX7_(+)" "PDX1_(+)"
## [190] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [193] "POLR3G_(+)" "POU3F2_(+)" "POU3F4_(+)"
## [196] "POU5F1_(+)" "PPARD_(+)" "PROX1_(+)"
## [199] "PRRX1_(+)" "PSMD12_(+)" "RARB_(+)"
## [202] "RARG_(+)" "RBBP5_(+)" "REL_(+)"
## [205] "RELA_(+)" "RFX1_(+)" "RFX2_(+)"
## [208] "RFX3_(+)" "RFX5_(+)" "RFXAP_(+)"
## [211] "SATB1_(+)" "SIN3A_(+)" "SIX2_(+)"
## [214] "SIX4_(+)" "SIX5_(+)" "SOHLH2_(+)"
## [217] "SOX1_(+)" "SOX13_(+)" "SOX15_(+)"
## [220] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [223] "SOX6_(+)" "SP7_(+)" "SP9_(+)"
## [226] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)"
## [229] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)"
## [232] "TBP_(+)" "TBPL1_(+)" "TBX15_(+)"
## [235] "TBX20_(+)" "TBX3_(+)" "TBX6_(+)"
## [238] "TCF4_(+)" "TCF7_(+)" "TET1_(+)"
## [241] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)"
## [244] "TFEB_(+)" "THAP1_(+)" "TLX2_(+)"
## [247] "TLX3_(+)" "TRPS1_(+)" "UQCRB_(+)"
## [250] "USF2_(+)" "VEZF1_(+)" "VSX1_(+)"
## [253] "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [256] "ZBTB41_(+)" "ZBTB43_(+)" "ZEB1_(+)"
## [259] "ZFHX2_(+)" "ZIC2_(+)" "ZNF160_(+)"
## [262] "ZNF189_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [265] "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)"
## [268] "ZNF281_(+)" "ZNF316_(+)" "ZNF441_(+)"
## [271] "ZNF442_(+)" "ZNF467_(+)" "ZNF471_(+)"
## [274] "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [277] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)"
## [280] "ZNF668_(+)" "ZNF713_(+)" "ZNF721_(+)"
## [283] "ZNF740_(+)" "ZNF816_(+)" "ZNF836_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $IAVdNS1_infected_NHBE
## [1] "AIRE_(+)" "ALX1_(+)" "AR_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [6] "ATF1_(+)" "ATF3_(+)" "ATF5_(+)" "BACH2_(+)" "BATF_(+)"
## [11] "BCL3_(+)" "BCLAF1_(+)" "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [16] "BNC2_(+)" "BRF1_(+)" "CCNT2_(+)" "CDX2_(+)" "CEBPA_(+)"
## [21] "CEBPB_(+)" "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)" "CKMT1B_(+)"
## [26] "CNOT3_(+)" "CPSF4_(+)" "CREB1_(+)" "CREB3_(+)" "CREB3L1_(+)"
## [31] "CTCF_(+)" "DBX1_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F3_(+)"
## [36] "E2F4_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)" "EGR2_(+)"
## [41] "EGR3_(+)" "ELK3_(+)" "EMX1_(+)" "EN2_(+)" "ENO1_(+)"
## [46] "EP300_(+)" "ERF_(+)" "ESR2_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [51] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)" "EVX2_(+)" "FGF19_(+)"
## [56] "FOS_(+)" "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)" "FOXB1_(+)"
## [61] "FOXC1_(+)" "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [66] "FOXD4L4_(+)" "FOXD4L6_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [71] "FOXO1_(+)" "FOXO3_(+)" "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [76] "GATA6_(+)" "GCM1_(+)" "GMEB1_(+)" "GMEB2_(+)" "GPD1_(+)"
## [81] "GRHL2_(+)" "GSX1_(+)" "GTF2IRD1_(+)" "HAND1_(+)" "HDAC1_(+)"
## [86] "HES5_(+)" "HIC1_(+)" "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [91] "HNF1B_(+)" "HOXA10_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [96] "HOXB13_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [101] "HOXC10_(+)" "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)" "HOXC8_(+)"
## [106] "HOXC9_(+)" "HOXD11_(+)" "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [111] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)" "IKZF3_(+)" "ING3_(+)"
## [116] "IRF1_(+)" "IRF4_(+)" "IRX2_(+)" "IRX5_(+)" "ISL2_(+)"
## [121] "JUN_(+)" "JUNB_(+)" "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [126] "KLF11_(+)" "KLF12_(+)" "KLF14_(+)" "KLF2_(+)" "KLF5_(+)"
## [131] "KLF8_(+)" "LHX4_(+)" "LHX8_(+)" "LHX9_(+)" "MAF_(+)"
## [136] "MAFB_(+)" "MAFF_(+)" "MAFG_(+)" "MEF2B_(+)" "MLXIP_(+)"
## [141] "MLXIPL_(+)" "MNT_(+)" "MNX1_(+)" "MSX1_(+)" "MSX2_(+)"
## [146] "MXD4_(+)" "MXI1_(+)" "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [151] "MZF1_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)" "NFIA_(+)"
## [156] "NFIB_(+)" "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)" "NHLH1_(+)"
## [161] "NHLH2_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [166] "NR1D1_(+)" "NR2C1_(+)" "NR2F1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [171] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)" "ONECUT2_(+)" "ONECUT3_(+)"
## [176] "OTP_(+)" "PATZ1_(+)" "PAX7_(+)" "PHF21A_(+)" "PKNOX1_(+)"
## [181] "POLE3_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU1F1_(+)"
## [186] "POU3F2_(+)" "POU3F4_(+)" "POU4F3_(+)" "POU5F1_(+)" "PPARD_(+)"
## [191] "PROX1_(+)" "PSMD12_(+)" "RARB_(+)" "RARG_(+)" "RBBP5_(+)"
## [196] "REL_(+)" "RELA_(+)" "RFX1_(+)" "RFX2_(+)" "RFX3_(+)"
## [201] "RFX5_(+)" "RFXAP_(+)" "SHOX2_(+)" "SIX4_(+)" "SIX5_(+)"
## [206] "SMAD3_(+)" "SNAPC4_(+)" "SOHLH2_(+)" "SOX1_(+)" "SOX13_(+)"
## [211] "SOX15_(+)" "SOX21_(+)" "SOX4_(+)" "SOX6_(+)" "SP9_(+)"
## [216] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)" "TAF7_(+)" "TAGLN2_(+)"
## [221] "TAL1_(+)" "TBP_(+)" "TBPL1_(+)" "TBX18_(+)" "TBX20_(+)"
## [226] "TBX3_(+)" "TCF4_(+)" "TCF7_(+)" "TEF_(+)" "TET1_(+)"
## [231] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)"
## [236] "TLX3_(+)" "TRPS1_(+)" "UBP1_(+)" "UBTF_(+)" "UQCRB_(+)"
## [241] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [246] "YY2_(+)" "ZBTB41_(+)" "ZBTB43_(+)" "ZDHHC15_(+)" "ZEB1_(+)"
## [251] "ZFHX2_(+)" "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)"
## [256] "ZNF143_(+)" "ZNF160_(+)" "ZNF205_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [261] "ZNF25_(+)" "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)" "ZNF281_(+)"
## [266] "ZNF316_(+)" "ZNF426_(+)" "ZNF441_(+)" "ZNF449_(+)" "ZNF467_(+)"
## [271] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [276] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)" "ZNF668_(+)" "ZNF713_(+)"
## [281] "ZNF717_(+)" "ZNF721_(+)" "ZNF740_(+)" "ZNF816_(+)" "ZNF841_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $RSV_infected_A549
## [1] "ARNT_(+)" "BCLAF1_(+)" "BHLHE40_(+)" "CDX1_(+)" "CLOCK_(+)"
## [6] "CREB5_(+)" "ELF2_(+)" "ELK3_(+)" "EP300_(+)" "ETV1_(+)"
## [11] "ETV3_(+)" "FOSL2_(+)" "GMEB1_(+)" "HEY1_(+)" "HOXB6_(+)"
## [16] "IRX2_(+)" "KLF7_(+)" "MAX_(+)" "MNX1_(+)" "MXD3_(+)"
## [21] "MYCN_(+)" "NFATC2_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)"
## [26] "NKX3-1_(+)" "NR2F1_(+)" "PKNOX1_(+)" "POLR3A_(+)" "POLR3G_(+)"
## [31] "PPARD_(+)" "PRDM16_(+)" "REL_(+)" "RREB1_(+)" "SMAD1_(+)"
## [36] "SNAI3_(+)" "SP5_(+)" "TCF7_(+)" "ZFX_(+)" "ZNF208_(+)"
## [41] "ZNF264_(+)" "ZNF267_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF502_(+)"
## [46] "ZNF560_(+)" "ZNF773_(+)"
##
## $SARSCoV2_infected_A549
## [1] "ALX1_(+)" "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)"
## [6] "ARNTL2_(+)" "ATF2_(+)" "ATF4_(+)" "ATF6_(+)" "BACH1_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHA15_(+)"
## [16] "BHLHE40_(+)" "BRF1_(+)" "CDX2_(+)" "CELF6_(+)" "CLOCK_(+)"
## [21] "CPEB1_(+)" "CTCFL_(+)" "DLX3_(+)" "DLX4_(+)" "DLX5_(+)"
## [26] "DRGX_(+)" "E2F1_(+)" "E2F2_(+)" "E2F4_(+)" "E2F5_(+)"
## [31] "EHF_(+)" "ELF1_(+)" "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [36] "EN1_(+)" "ERF_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)"
## [41] "ETV3_(+)" "FEV_(+)" "FLI1_(+)" "FOSL2_(+)" "FOXA3_(+)"
## [46] "FOXD2_(+)" "FOXD3_(+)" "FOXF2_(+)" "FOXP4_(+)" "FOXQ1_(+)"
## [51] "GABPA_(+)" "GABPB1_(+)" "GATA5_(+)" "GCM1_(+)" "GLI1_(+)"
## [56] "GLIS2_(+)" "GRHL3_(+)" "GRHPR_(+)" "GSX2_(+)" "GTF2B_(+)"
## [61] "GTF2IRD1_(+)" "GTF3A_(+)" "HES5_(+)" "HES6_(+)" "HEY1_(+)"
## [66] "HIC1_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)" "HOXA1_(+)"
## [71] "HOXA6_(+)" "HOXA7_(+)" "HOXB13_(+)" "HOXB2_(+)" "HOXB5_(+)"
## [76] "HOXB6_(+)" "HOXB8_(+)" "HOXC10_(+)" "HOXC11_(+)" "HOXC6_(+)"
## [81] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [86] "IKZF2_(+)" "ING3_(+)" "IRF2_(+)" "IRF6_(+)" "IRF9_(+)"
## [91] "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "JUND_(+)" "KLF10_(+)"
## [96] "KLF6_(+)" "KLF7_(+)" "KLF8_(+)" "LBX2_(+)" "LHX2_(+)"
## [101] "LMX1B_(+)" "MAF_(+)" "MAFA_(+)" "MAX_(+)" "MAZ_(+)"
## [106] "MECOM_(+)" "MEOX1_(+)" "MESP1_(+)" "MNX1_(+)" "MXD1_(+)"
## [111] "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [116] "MZF1_(+)" "NEUROD1_(+)" "NFATC4_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [121] "NFIB_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)"
## [126] "NKX2-1_(+)" "NKX2-5_(+)" "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [131] "NR2E1_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR6A1_(+)" "ONECUT2_(+)"
## [136] "OTP_(+)" "OTX1_(+)" "PATZ1_(+)" "PAX7_(+)" "PAX9_(+)"
## [141] "PHF8_(+)" "PKNOX1_(+)" "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)"
## [146] "POLR3G_(+)" "POU3F4_(+)" "PRDM1_(+)" "PRDM15_(+)" "PRRX2_(+)"
## [151] "PSMD12_(+)" "RAB18_(+)" "RB1_(+)" "RFX1_(+)" "RFX2_(+)"
## [156] "RREB1_(+)" "RUNX2_(+)" "RXRG_(+)" "SATB1_(+)" "SHOX2_(+)"
## [161] "SIN3A_(+)" "SIX5_(+)" "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [166] "SNAI1_(+)" "SNAI2_(+)" "SNAI3_(+)" "SOX5_(+)" "SP3_(+)"
## [171] "SP5_(+)" "SPDEF_(+)" "STAT1_(+)" "STAT5B_(+)" "TAL2_(+)"
## [176] "TCF3_(+)" "TCF7L1_(+)" "TCF7L2_(+)" "TEAD2_(+)" "TFAP2A_(+)"
## [181] "TFAP2C_(+)" "TFDP2_(+)" "THRA_(+)" "TLX1_(+)" "TLX2_(+)"
## [186] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VSX2_(+)"
## [191] "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)" "ZNF134_(+)"
## [196] "ZNF143_(+)" "ZNF219_(+)" "ZNF267_(+)" "ZNF281_(+)" "ZNF319_(+)"
## [201] "ZNF35_(+)" "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)"
## [206] "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)" "ZNF524_(+)"
## [211] "ZNF554_(+)" "ZNF560_(+)" "ZNF583_(+)" "ZNF597_(+)" "ZNF672_(+)"
## [216] "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)" "ZNF75A_(+)" "ZNF768_(+)"
## [221] "ZNF773_(+)" "ZNF787_(+)"
##
## $SARSCoV2_infected_A549_hACE2
## [1] "ATF3_(+)" "CEBPD_(+)" "DLX2_(+)" "EGR3_(+)" "EMX1_(+)"
## [6] "ETV6_(+)" "ETV7_(+)" "FOXK1_(+)" "HIVEP2_(+)" "HOXB6_(+)"
## [11] "IRF1_(+)" "IRF5_(+)" "IRF8_(+)" "IRF9_(+)" "KLF13_(+)"
## [16] "MEF2B_(+)" "NEUROD2_(+)" "NFE2L2_(+)" "NKX3-1_(+)" "RXRG_(+)"
## [21] "SMARCA5_(+)" "SOX2_(+)" "SOX21_(+)" "STAT1_(+)" "STAT2_(+)"
## [26] "TP53_(+)" "TP73_(+)" "XBP1_(+)" "ZNF768_(+)"
##
## $SARSCoV2_infected_A549_hACE2_pt
## [1] "AIRE_(+)" "AKR1A1_(+)" "ALX4_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF3_(+)" "BCLAF1_(+)" "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"
## [11] "CDX2_(+)" "CEBPA_(+)" "CEBPD_(+)" "CLOCK_(+)" "CTCFL_(+)"
## [16] "DLX2_(+)" "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)"
## [21] "E2F1_(+)" "E2F2_(+)" "E2F7_(+)" "E2F8_(+)" "EBF1_(+)"
## [26] "EGR1_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELK3_(+)"
## [31] "ELK4_(+)" "EMX1_(+)" "ENO1_(+)" "ERF_(+)" "ETS1_(+)"
## [36] "ETS2_(+)" "ETV6_(+)" "ETV7_(+)" "FOSB_(+)" "FOSL2_(+)"
## [41] "FOXB1_(+)" "FOXD3_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [46] "FOXN1_(+)" "FOXO1_(+)" "FOXP1_(+)" "GATA5_(+)" "GLI1_(+)"
## [51] "GRHPR_(+)" "GSC2_(+)" "GTF2B_(+)" "HES6_(+)" "HEY1_(+)"
## [56] "HIVEP2_(+)" "HLX_(+)" "HNF4G_(+)" "HOXA2_(+)" "HOXA6_(+)"
## [61] "HOXA9_(+)" "HOXB1_(+)" "HOXB6_(+)" "HOXC11_(+)" "HOXC5_(+)"
## [66] "HOXC9_(+)" "HOXD4_(+)" "HSF1_(+)" "IKZF2_(+)" "IRF1_(+)"
## [71] "IRF2_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [76] "IRF9_(+)" "IRX5_(+)" "JUND_(+)" "KDM4D_(+)" "KLF13_(+)"
## [81] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)" "LHX1_(+)" "LHX2_(+)"
## [86] "LMX1B_(+)" "MAFB_(+)" "MAX_(+)" "MAZ_(+)" "MLXIP_(+)"
## [91] "MLXIPL_(+)" "MNX1_(+)" "MXD3_(+)" "MYCN_(+)" "MYEF2_(+)"
## [96] "MZF1_(+)" "NEUROD2_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [101] "NFKB1_(+)" "NKX2-2_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR1D1_(+)"
## [106] "NR1H3_(+)" "NR1H4_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR3C2_(+)"
## [111] "NR4A1_(+)" "ONECUT2_(+)" "PBX3_(+)" "PDX1_(+)" "PHF21A_(+)"
## [116] "POLE4_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F3_(+)" "POU3F1_(+)"
## [121] "POU3F4_(+)" "PPARD_(+)" "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [126] "REL_(+)" "RFX1_(+)" "RFXAP_(+)" "RUNX2_(+)" "RXRG_(+)"
## [131] "SATB1_(+)" "SETDB1_(+)" "SHOX2_(+)" "SIX2_(+)" "SIX5_(+)"
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)" "SOX2_(+)" "SOX21_(+)"
## [141] "SOX9_(+)" "SP6_(+)" "SREBF1_(+)" "STAT1_(+)" "STAT2_(+)"
## [146] "STAT5B_(+)" "TAF1_(+)" "TBX20_(+)" "TBX3_(+)" "TCF12_(+)"
## [151] "TEAD2_(+)" "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)" "TGIF1_(+)"
## [156] "TP73_(+)" "TRIM28_(+)" "TWIST1_(+)" "USF1_(+)" "VAX1_(+)"
## [161] "VEZF1_(+)" "XBP1_(+)" "ZBED1_(+)" "ZBTB41_(+)" "ZFHX3_(+)"
## [166] "ZFX_(+)" "ZNF239_(+)" "ZNF274_(+)" "ZNF276_(+)" "ZNF460_(+)"
## [171] "ZNF502_(+)" "ZNF524_(+)" "ZNF579_(+)" "ZNF583_(+)" "ZNF652_(+)"
## [176] "ZNF668_(+)" "ZNF672_(+)" "ZNF701_(+)" "ZNF721_(+)" "ZNF730_(+)"
## [181] "ZNF768_(+)" "ZNF773_(+)" "ZNF787_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_Calu3
## [1] "AKR1A1_(+)" "ALX4_(+)" "AR_(+)"
## [4] "ARID3C_(+)" "ARID5B_(+)" "ARNT_(+)"
## [7] "ARNT2_(+)" "ARNTL_(+)" "ARNTL2_(+)"
## [10] "ARX_(+)" "ASCL1_(+)" "ASCL2_(+)"
## [13] "ATF3_(+)" "ATF4_(+)" "ATF6_(+)"
## [16] "ATF6B_(+)" "BACH2_(+)" "BATF_(+)"
## [19] "BBX_(+)" "BCL11A_(+)" "BCL3_(+)"
## [22] "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [25] "BNC2_(+)" "BORCS8-MEF2B_(+)" "BRCA1_(+)"
## [28] "BRF2_(+)" "CCNT2_(+)" "CDX2_(+)"
## [31] "CEBPD_(+)" "CEBPG_(+)" "CIC_(+)"
## [34] "CPEB1_(+)" "CREB3L1_(+)" "CREB5_(+)"
## [37] "CREBL2_(+)" "CTCF_(+)" "CUX1_(+)"
## [40] "DBP_(+)" "DDIT3_(+)" "DLX2_(+)"
## [43] "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)"
## [46] "DRGX_(+)" "DUX4_(+)" "DUXA_(+)"
## [49] "E2F1_(+)" "E2F2_(+)" "E2F8_(+)"
## [52] "E4F1_(+)" "EGR2_(+)" "EGR3_(+)"
## [55] "EHF_(+)" "ELF1_(+)" "ELF4_(+)"
## [58] "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [61] "EMX1_(+)" "ENO1_(+)" "EOMES_(+)"
## [64] "EP300_(+)" "ESRRA_(+)" "ESX1_(+)"
## [67] "ETS1_(+)" "ETS2_(+)" "ETV3_(+)"
## [70] "ETV4_(+)" "ETV6_(+)" "ETV7_(+)"
## [73] "EVX2_(+)" "FBXL19_(+)" "FEV_(+)"
## [76] "FOSB_(+)" "FOSL1_(+)" "FOSL2_(+)"
## [79] "FOXA2_(+)" "FOXA3_(+)" "FOXC1_(+)"
## [82] "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)"
## [85] "FOXD4L6_(+)" "FOXF1_(+)" "FOXF2_(+)"
## [88] "FOXG1_(+)" "FOXJ2_(+)" "FOXJ3_(+)"
## [91] "FOXK1_(+)" "FOXL1_(+)" "FOXM1_(+)"
## [94] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [97] "FOXO4_(+)" "GABPB1_(+)" "GATA2_(+)"
## [100] "GATA3_(+)" "GATA5_(+)" "GATA6_(+)"
## [103] "GBX1_(+)" "GLI1_(+)" "GLIS2_(+)"
## [106] "GMEB1_(+)" "GMEB2_(+)" "GRHL1_(+)"
## [109] "GRHL2_(+)" "GRHPR_(+)" "GSC_(+)"
## [112] "GSC2_(+)" "GTF2B_(+)" "GTF2IRD1_(+)"
## [115] "GTF3A_(+)" "HAND1_(+)" "HDAC2_(+)"
## [118] "HES1_(+)" "HES5_(+)" "HES6_(+)"
## [121] "HESX1_(+)" "HEY2_(+)" "HINFP_(+)"
## [124] "HIVEP1_(+)" "HIVEP2_(+)" "HLF_(+)"
## [127] "HLX_(+)" "HMGB1_(+)" "HNF1A_(+)"
## [130] "HOXA2_(+)" "HOXA6_(+)" "HOXA9_(+)"
## [133] "HOXB4_(+)" "HOXB6_(+)" "HOXB7_(+)"
## [136] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [139] "HOXC11_(+)" "HOXC13_(+)" "HOXC4_(+)"
## [142] "HOXC6_(+)" "HOXC8_(+)" "HOXD1_(+)"
## [145] "HOXD10_(+)" "HOXD4_(+)" "HOXD8_(+)"
## [148] "HOXD9_(+)" "HSF1_(+)" "HSF2_(+)"
## [151] "IKZF2_(+)" "ING3_(+)" "IRF1_(+)"
## [154] "IRF2_(+)" "IRF4_(+)" "IRF5_(+)"
## [157] "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [160] "IRF9_(+)" "IRX2_(+)" "ISL2_(+)"
## [163] "JUN_(+)" "JUND_(+)" "KDM4D_(+)"
## [166] "KDM5A_(+)" "KLF10_(+)" "KLF11_(+)"
## [169] "KLF12_(+)" "KLF13_(+)" "KLF14_(+)"
## [172] "KLF15_(+)" "KLF16_(+)" "KLF2_(+)"
## [175] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)"
## [178] "KLF8_(+)" "KLF9_(+)" "LBX1_(+)"
## [181] "LHX1_(+)" "LHX4_(+)" "LHX5_(+)"
## [184] "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)"
## [187] "MAFK_(+)" "MAX_(+)" "MAZ_(+)"
## [190] "MECOM_(+)" "MEF2C_(+)" "MEIS1_(+)"
## [193] "MEOX2_(+)" "MESP1_(+)" "MIOS_(+)"
## [196] "MITF_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [199] "MXI1_(+)" "MYBL1_(+)" "MYCN_(+)"
## [202] "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [205] "MZF1_(+)" "NEUROD1_(+)" "NFATC2_(+)"
## [208] "NFE2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [211] "NFE2L3_(+)" "NFIC_(+)" "NFKB1_(+)"
## [214] "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)"
## [217] "NHLH2_(+)" "NKX3-1_(+)" "NKX6-2_(+)"
## [220] "NPAS2_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [223] "NR1H2_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [226] "NR1I2_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [229] "NR2F6_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [232] "NRF1_(+)" "OLIG2_(+)" "OLIG3_(+)"
## [235] "ONECUT2_(+)" "OTP_(+)" "OVOL1_(+)"
## [238] "PAX7_(+)" "PAX8_(+)" "PAX9_(+)"
## [241] "PBX1_(+)" "PDX1_(+)" "PHF2_(+)"
## [244] "PHF21A_(+)" "PHF8_(+)" "PHOX2A_(+)"
## [247] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [250] "POLR3A_(+)" "POU2F1_(+)" "POU4F1_(+)"
## [253] "POU5F1_(+)" "POU5F1B_(+)" "POU6F1_(+)"
## [256] "PPARA_(+)" "PPARD_(+)" "PRDM1_(+)"
## [259] "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [262] "RAD21_(+)" "RARA_(+)" "RARG_(+)"
## [265] "RBBP5_(+)" "REL_(+)" "RFX7_(+)"
## [268] "RREB1_(+)" "RUNX2_(+)" "SATB1_(+)"
## [271] "SETDB1_(+)" "SHOX2_(+)" "SIN3A_(+)"
## [274] "SIX1_(+)" "SIX2_(+)" "SIX5_(+)"
## [277] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [280] "SMC3_(+)" "SNAI3_(+)" "SNAPC4_(+)"
## [283] "SOX11_(+)" "SOX13_(+)" "SOX15_(+)"
## [286] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [289] "SOX9_(+)" "SP1_(+)" "SP2_(+)"
## [292] "SP6_(+)" "SP7_(+)" "SP9_(+)"
## [295] "SPDEF_(+)" "SREBF2_(+)" "SRF_(+)"
## [298] "STAT1_(+)" "STAT2_(+)" "STAT4_(+)"
## [301] "STAT5B_(+)" "STAU2_(+)" "TAF7_(+)"
## [304] "TAL1_(+)" "TBP_(+)" "TBPL2_(+)"
## [307] "TBX15_(+)" "TBX18_(+)" "TBX20_(+)"
## [310] "TBX6_(+)" "TCF3_(+)" "TCF4_(+)"
## [313] "TCF7_(+)" "TCF7L1_(+)" "TEAD4_(+)"
## [316] "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)"
## [319] "TFDP1_(+)" "TFDP2_(+)" "TFE3_(+)"
## [322] "TFEB_(+)" "TGIF2_(+)" "THAP1_(+)"
## [325] "TLX1_(+)" "TLX2_(+)" "TP73_(+)"
## [328] "TRIM28_(+)" "UBP1_(+)" "USF1_(+)"
## [331] "VAX1_(+)" "VAX2_(+)" "VDR_(+)"
## [334] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)"
## [337] "WT1_(+)" "YBX1_(+)" "YY2_(+)"
## [340] "ZBTB33_(+)" "ZEB1_(+)" "ZFHX2_(+)"
## [343] "ZFY_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [346] "ZNF160_(+)" "ZNF208_(+)" "ZNF219_(+)"
## [349] "ZNF25_(+)" "ZNF264_(+)" "ZNF267_(+)"
## [352] "ZNF276_(+)" "ZNF316_(+)" "ZNF354C_(+)"
## [355] "ZNF384_(+)" "ZNF429_(+)" "ZNF441_(+)"
## [358] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)"
## [361] "ZNF513_(+)" "ZNF524_(+)" "ZNF550_(+)"
## [364] "ZNF554_(+)" "ZNF560_(+)" "ZNF606_(+)"
## [367] "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [370] "ZNF713_(+)" "ZNF717_(+)" "ZNF721_(+)"
## [373] "ZNF761_(+)" "ZNF768_(+)" "ZNF787_(+)"
## [376] "ZNF8_(+)" "ZSCAN31_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF1_(+)" "BATF_(+)" "BBX_(+)" "BCL3_(+)" "BCL6B_(+)"
## [11] "CEBPB_(+)" "CEBPG_(+)" "CKMT1B_(+)" "CREB1_(+)" "CREB3_(+)"
## [16] "CREBL2_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [21] "EBF1_(+)" "EGR2_(+)" "ERF_(+)" "ESRRA_(+)" "ETV1_(+)"
## [26] "ETV6_(+)" "ETV7_(+)" "FOSL1_(+)" "FOXA2_(+)" "FOXF2_(+)"
## [31] "FOXK2_(+)" "FOXP3_(+)" "FOXQ1_(+)" "GATA2_(+)" "GATA3_(+)"
## [36] "HDAC2_(+)" "HES5_(+)" "HLF_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [41] "HOXA2_(+)" "HOXA5_(+)" "HOXA7_(+)" "HOXA9_(+)" "HOXB5_(+)"
## [46] "HOXB6_(+)" "HOXB7_(+)" "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [51] "HOXC4_(+)" "HOXC5_(+)" "HOXC6_(+)" "HOXC8_(+)" "HSF2_(+)"
## [56] "ING3_(+)" "IRF1_(+)" "IRF3_(+)" "IRF4_(+)" "IRF5_(+)"
## [61] "IRF8_(+)" "IRF9_(+)" "IRX2_(+)" "ISL2_(+)" "JUN_(+)"
## [66] "KLF10_(+)" "KLF5_(+)" "LHX1_(+)" "LHX4_(+)" "LHX8_(+)"
## [71] "LHX9_(+)" "MAFF_(+)" "MEOX2_(+)" "MIOS_(+)" "MLXIP_(+)"
## [76] "MSX1_(+)" "MSX2_(+)" "MXD4_(+)" "MYEF2_(+)" "NFIL3_(+)"
## [81] "NFYB_(+)" "NHLH1_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NR1I2_(+)"
## [86] "NR4A1_(+)" "NRF1_(+)" "ONECUT2_(+)" "OVOL2_(+)" "PAX2_(+)"
## [91] "PAX7_(+)" "PBX1_(+)" "PDX1_(+)" "PKNOX1_(+)" "POU2F3_(+)"
## [96] "PRDM16_(+)" "RARG_(+)" "RBBP5_(+)" "RELA_(+)" "RFX5_(+)"
## [101] "SIX2_(+)" "SMC3_(+)" "SOX13_(+)" "SOX2_(+)" "SP1_(+)"
## [106] "SP2_(+)" "SP4_(+)" "SP7_(+)" "SREBF2_(+)" "STAT1_(+)"
## [111] "STAT2_(+)" "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBP_(+)"
## [116] "TBPL1_(+)" "TBPL2_(+)" "TBX15_(+)" "TBX3_(+)" "TCF7_(+)"
## [121] "TET1_(+)" "TFAP2A_(+)" "TFE3_(+)" "TFEB_(+)" "TLX3_(+)"
## [126] "TWIST1_(+)" "UBTF_(+)" "UQCRB_(+)" "VSX1_(+)" "WT1_(+)"
## [131] "ZEB1_(+)" "ZFHX2_(+)" "ZFY_(+)" "ZNF160_(+)" "ZNF471_(+)"
## [136] "ZNF502_(+)" "ZNF560_(+)" "ZNF580_(+)" "ZNF768_(+)" "ZNF773_(+)"
## [141] "ZXDC_(+)"
##
## $human_IFNB_treated_NHBE
## [1] "ATF3_(+)" "BACH2_(+)" "ELF3_(+)" "ETV6_(+)" "ETV7_(+)"
## [6] "FOXA1_(+)" "FOXK1_(+)" "GATA2_(+)" "GCM1_(+)" "GTF2B_(+)"
## [11] "HIVEP2_(+)" "HLX_(+)" "HOXD11_(+)" "IRF1_(+)" "IRF2_(+)"
## [16] "IRF7_(+)" "IRF8_(+)" "IRF9_(+)" "NFIL3_(+)" "NFIX_(+)"
## [21] "NKX3-1_(+)" "POU5F1B_(+)" "PRDM16_(+)" "RARA_(+)" "RELA_(+)"
## [26] "RXRB_(+)" "SOX11_(+)" "SOX9_(+)" "STAT2_(+)" "TFEB_(+)"
## [31] "VEZF1_(+)"# Load and tidy data: adjusted pvalues, format
paste0("using pvalues from test : ", params$adj_pvals_mwu.fn)## [1] "using pvalues from test : pvalues-mwu-2t-adjusted.csv"pvalues <- as.data.frame(read_csv(paste0(params$inputdir,params$adj_pvals_mwu.fn), col_names = T))
if(params$celllines==1){
names(pvalues) <- str_replace_all(names(pvalues), "-", "")
names(pvalues) <- str_replace(names(pvalues), "w_vector_expressing_", "")
names(pvalues) <- str_replace(names(pvalues), "1hr_Ruxolitinib_pretreatment", "pt")
}
rownames(pvalues) <- tfs
## Graph a Volcano Plot per condition
plots <- volcanos_per_exp(pvalues = pvalues, tfs_da = tfs_da,
test = "2t", save_png=T, outdir = params$outdir)## [1] "HPIV3_infected_A549"## [1] "IAV_infected_A549"## [1] "IAV_infected_NHBE"## [1] "IAVdNS1_infected_NHBE"## [1] "RSV_infected_A549"## [1] "SARSCoV2_infected_A549"## [1] "SARSCoV2_infected_A549_hACE2"## [1] "SARSCoV2_infected_A549_hACE2_pt"## [1] "SARSCoV2_infected_Calu3"## [1] "SARSCoV2_infected_NHBE"## [1] "human_IFNB_treated_NHBE"plots## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
## NULL
##
## [[6]]
## NULL
##
## [[7]]
## NULL
##
## [[8]]
## NULL
##
## [[9]]
## NULL
##
## [[10]]
## NULL
##
## [[11]]
## NULL
##
## $HPIV3_infected_A549
##
## $IAV_infected_A549
##
## $IAV_infected_NHBE
##
## $IAVdNS1_infected_NHBE
##
## $RSV_infected_A549
##
## $SARSCoV2_infected_A549
##
## $SARSCoV2_infected_A549_hACE2
##
## $SARSCoV2_infected_A549_hACE2_pt
##
## $SARSCoV2_infected_Calu3
##
## $SARSCoV2_infected_NHBE
##
## $human_IFNB_treated_NHBE
############################################
## Make lists of up/down regulons
tfs_da_up = list()
tfs_da_down = list()
for (exp in names(tfs_da)) {
tfs_da_up[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc[exp] > 0)]
tfs_da_down[[exp]] <- tfs_da[[exp]][tfs_da[[exp]] %in% rownames(l2fc[exp] > 0)]
}
tfs_da_up## $HPIV3_infected_A549
## [1] "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNTL_(+)" "ATF1_(+)"
## [6] "ATF4_(+)" "ATF5_(+)" "BCL6B_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [11] "BRF1_(+)" "CDX1_(+)" "CHD2_(+)" "CLOCK_(+)" "CPEB1_(+)"
## [16] "CREB1_(+)" "CREB5_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F1_(+)"
## [21] "E4F1_(+)" "ELF2_(+)" "ESRRA_(+)" "FOSL1_(+)" "FOXA2_(+)"
## [26] "FOXB1_(+)" "FOXC2_(+)" "FOXF2_(+)" "FOXK1_(+)" "FOXO1_(+)"
## [31] "FOXO3_(+)" "FOXP2_(+)" "GABPB1_(+)" "GCM1_(+)" "HAND1_(+)"
## [36] "HES6_(+)" "HEY1_(+)" "HEY2_(+)" "HIVEP2_(+)" "HLF_(+)"
## [41] "HOXA9_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [46] "HOXC10_(+)" "HOXC13_(+)" "HOXC8_(+)" "HOXD11_(+)" "HSF2_(+)"
## [51] "IKZF2_(+)" "IRF4_(+)" "ISL2_(+)" "KDM5A_(+)" "KLF3_(+)"
## [56] "KLF7_(+)" "KLF9_(+)" "LHX4_(+)" "MAF_(+)" "MAZ_(+)"
## [61] "MECOM_(+)" "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)"
## [66] "NEUROD1_(+)" "NFE2L1_(+)" "NFIA_(+)" "NFIL3_(+)" "NFKB1_(+)"
## [71] "NFKB2_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)" "NKX3-1_(+)"
## [76] "NR2C1_(+)" "NR5A2_(+)" "OTP_(+)" "PAX7_(+)" "POU3F2_(+)"
## [81] "POU5F1_(+)" "RARB_(+)" "RFX2_(+)" "RFX3_(+)" "RREB1_(+)"
## [86] "RUNX2_(+)" "SNAI3_(+)" "SOX1_(+)" "SOX15_(+)" "SP6_(+)"
## [91] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBX15_(+)" "TBX20_(+)"
## [96] "TCF3_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)" "VSX1_(+)"
## [101] "ZBTB33_(+)" "ZBTB7A_(+)" "ZEB1_(+)" "ZFX_(+)" "ZIC2_(+)"
## [106] "ZNF134_(+)" "ZNF143_(+)" "ZNF148_(+)" "ZNF160_(+)" "ZNF227_(+)"
## [111] "ZNF354C_(+)" "ZNF429_(+)" "ZNF449_(+)" "ZNF502_(+)" "ZNF524_(+)"
## [116] "ZNF571_(+)" "ZNF597_(+)" "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [121] "ZNF787_(+)" "ZNF841_(+)" "ZSCAN26_(+)"
##
## $IAV_infected_A549
## [1] "ALX1_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)" "ARNTL2_(+)"
## [6] "ASCL2_(+)" "ATF2_(+)" "ATF4_(+)" "BACH1_(+)" "BATF_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHE40_(+)"
## [16] "BRF1_(+)" "CDX2_(+)" "CLOCK_(+)" "CPEB1_(+)" "CREB5_(+)"
## [21] "CTCFL_(+)" "DLX3_(+)" "DLX5_(+)" "E2F1_(+)" "E2F2_(+)"
## [26] "E2F4_(+)" "E2F5_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)"
## [31] "EGR3_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELF5_(+)"
## [36] "ELK3_(+)" "ELK4_(+)" "EN1_(+)" "EN2_(+)" "ERF_(+)"
## [41] "ESRRA_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)" "ETV7_(+)"
## [46] "FOSB_(+)" "FOSL2_(+)" "FOXB1_(+)" "FOXC1_(+)" "FOXD3_(+)"
## [51] "FOXF2_(+)" "FOXM1_(+)" "FOXO1_(+)" "GABPA_(+)" "GABPB1_(+)"
## [56] "GATA5_(+)" "GCM1_(+)" "GLI1_(+)" "GLIS2_(+)" "GRHL1_(+)"
## [61] "GRHL3_(+)" "GRHPR_(+)" "GSC_(+)" "GSX2_(+)" "GTF2B_(+)"
## [66] "GTF2IRD1_(+)" "HES1_(+)" "HES5_(+)" "HES6_(+)" "HIC1_(+)"
## [71] "HINFP_(+)" "HIVEP2_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [76] "HOXA1_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA6_(+)" "HOXA7_(+)"
## [81] "HOXA9_(+)" "HOXB13_(+)" "HOXB5_(+)" "HOXB7_(+)" "HOXB8_(+)"
## [86] "HOXC10_(+)" "HOXC11_(+)" "HOXC13_(+)" "HOXC5_(+)" "HOXC6_(+)"
## [91] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HTATIP2_(+)" "IRF1_(+)"
## [96] "IRF2_(+)" "IRF3_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)"
## [101] "IRF9_(+)" "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "IRX5_(+)"
## [106] "JUND_(+)" "KLF10_(+)" "KLF3_(+)" "KLF4_(+)" "KLF5_(+)"
## [111] "KLF6_(+)" "KLF8_(+)" "KLF9_(+)" "LBX2_(+)" "LHX2_(+)"
## [116] "LHX5_(+)" "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)" "MAFG_(+)"
## [121] "MAX_(+)" "MAZ_(+)" "MECOM_(+)" "MEOX1_(+)" "MNX1_(+)"
## [126] "MSX2_(+)" "MTF1_(+)" "MXD1_(+)" "MXD3_(+)" "MXD4_(+)"
## [131] "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)" "MYPOP_(+)" "MZF1_(+)"
## [136] "NEUROD1_(+)" "NFATC4_(+)" "NFE2_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [141] "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)" "NKX2-1_(+)"
## [146] "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [151] "NR2F6_(+)" "ONECUT2_(+)" "OTP_(+)" "OTX1_(+)" "OVOL2_(+)"
## [156] "PAX7_(+)" "PAX9_(+)" "PHF21A_(+)" "PHF8_(+)" "PKNOX1_(+)"
## [161] "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F1_(+)"
## [166] "POU2F3_(+)" "POU3F1_(+)" "POU3F4_(+)" "PPARD_(+)" "PRDM1_(+)"
## [171] "PRDM15_(+)" "PRRX2_(+)" "PSMD12_(+)" "RAB18_(+)" "RARG_(+)"
## [176] "REL_(+)" "RFX2_(+)" "RORA_(+)" "RREB1_(+)" "RXRG_(+)"
## [181] "SATB1_(+)" "SETDB1_(+)" "SIN3A_(+)" "SIX2_(+)" "SIX5_(+)"
## [186] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)" "SNAI2_(+)" "SNAI3_(+)"
## [191] "SOX5_(+)" "SP3_(+)" "SP5_(+)" "STAT1_(+)" "STAT2_(+)"
## [196] "STAT5A_(+)" "STAT5B_(+)" "TAGLN2_(+)" "TBPL2_(+)" "TCF12_(+)"
## [201] "TCF3_(+)" "TCF7_(+)" "TEAD4_(+)" "TEF_(+)" "TFAP2A_(+)"
## [206] "TFAP2C_(+)" "TFAP2E_(+)" "TFDP2_(+)" "TGIF2_(+)" "TLX2_(+)"
## [211] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VDR_(+)"
## [216] "VSX2_(+)" "ZBTB7A_(+)" "ZFX_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [221] "ZNF208_(+)" "ZNF219_(+)" "ZNF274_(+)" "ZNF281_(+)" "ZNF35_(+)"
## [226] "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)" "ZNF483_(+)"
## [231] "ZNF502_(+)" "ZNF524_(+)" "ZNF554_(+)" "ZNF560_(+)" "ZNF597_(+)"
## [236] "ZNF672_(+)" "ZNF682_(+)" "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)"
## [241] "ZNF761_(+)" "ZNF773_(+)" "ZNF787_(+)"
##
## $IAV_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)"
## [4] "ALX3_(+)" "ALX4_(+)" "AR_(+)"
## [7] "ARID5B_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [10] "ATF1_(+)" "ATF3_(+)" "BACH2_(+)"
## [13] "BATF_(+)" "BCL3_(+)" "BCLAF1_(+)"
## [16] "BDP1_(+)" "BHLHE41_(+)" "BNC2_(+)"
## [19] "BORCS8-MEF2B_(+)" "BRF1_(+)" "CCNT2_(+)"
## [22] "CDX2_(+)" "CEBPA_(+)" "CEBPB_(+)"
## [25] "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)"
## [28] "CKMT1B_(+)" "CLOCK_(+)" "CNOT3_(+)"
## [31] "CPEB1_(+)" "CPSF4_(+)" "CREB1_(+)"
## [34] "CREB3_(+)" "CREB3L1_(+)" "CUX1_(+)"
## [37] "DBX1_(+)" "DLX2_(+)" "DLX4_(+)"
## [40] "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [43] "E2F3_(+)" "E2F4_(+)" "E2F6_(+)"
## [46] "EGR1_(+)" "EGR2_(+)" "EGR3_(+)"
## [49] "ELK3_(+)" "EMX1_(+)" "EN1_(+)"
## [52] "EN2_(+)" "ENO1_(+)" "EP300_(+)"
## [55] "ERF_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [58] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)"
## [61] "EVX2_(+)" "FGF19_(+)" "FOS_(+)"
## [64] "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)"
## [67] "FOXB1_(+)" "FOXC1_(+)" "FOXC2_(+)"
## [70] "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [73] "FOXD4L6_(+)" "FOXF2_(+)" "FOXJ2_(+)"
## [76] "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [79] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [82] "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [85] "GCM1_(+)" "GLIS2_(+)" "GMEB1_(+)"
## [88] "GRHL2_(+)" "GTF2IRD1_(+)" "HAND1_(+)"
## [91] "HDAC1_(+)" "HES5_(+)" "HEY1_(+)"
## [94] "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [97] "HNF1A_(+)" "HNF1B_(+)" "HOXA10_(+)"
## [100] "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [103] "HOXB13_(+)" "HOXB4_(+)" "HOXB6_(+)"
## [106] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [109] "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)"
## [112] "HOXC8_(+)" "HOXC9_(+)" "HOXD11_(+)"
## [115] "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [118] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [121] "IKZF3_(+)" "ING3_(+)" "IRF1_(+)"
## [124] "IRF4_(+)" "IRX2_(+)" "IRX5_(+)"
## [127] "ISL2_(+)" "JUN_(+)" "JUNB_(+)"
## [130] "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [133] "KLF10_(+)" "KLF11_(+)" "KLF12_(+)"
## [136] "KLF13_(+)" "KLF14_(+)" "KLF2_(+)"
## [139] "KLF5_(+)" "KLF8_(+)" "LHX4_(+)"
## [142] "LHX8_(+)" "LHX9_(+)" "LMX1B_(+)"
## [145] "MAF_(+)" "MAFB_(+)" "MAFF_(+)"
## [148] "MAFG_(+)" "MEF2B_(+)" "MEF2C_(+)"
## [151] "MEOX2_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [154] "MNT_(+)" "MNX1_(+)" "MSX1_(+)"
## [157] "MSX2_(+)" "MYEF2_(+)" "MYOD1_(+)"
## [160] "MZF1_(+)" "NFATC2_(+)" "NFE2L2_(+)"
## [163] "NFE2L3_(+)" "NFIA_(+)" "NFIB_(+)"
## [166] "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)"
## [169] "NHLH1_(+)" "NKX2-1_(+)" "NKX2-5_(+)"
## [172] "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [175] "NR1D1_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [178] "NR3C1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [181] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)"
## [184] "ONECUT2_(+)" "ONECUT3_(+)" "OTP_(+)"
## [187] "PATZ1_(+)" "PAX7_(+)" "PDX1_(+)"
## [190] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [193] "POLR3G_(+)" "POU3F2_(+)" "POU3F4_(+)"
## [196] "POU5F1_(+)" "PPARD_(+)" "PROX1_(+)"
## [199] "PRRX1_(+)" "PSMD12_(+)" "RARB_(+)"
## [202] "RARG_(+)" "RBBP5_(+)" "REL_(+)"
## [205] "RELA_(+)" "RFX1_(+)" "RFX2_(+)"
## [208] "RFX3_(+)" "RFX5_(+)" "RFXAP_(+)"
## [211] "SATB1_(+)" "SIN3A_(+)" "SIX2_(+)"
## [214] "SIX4_(+)" "SIX5_(+)" "SOHLH2_(+)"
## [217] "SOX1_(+)" "SOX13_(+)" "SOX15_(+)"
## [220] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [223] "SOX6_(+)" "SP7_(+)" "SP9_(+)"
## [226] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)"
## [229] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)"
## [232] "TBP_(+)" "TBPL1_(+)" "TBX15_(+)"
## [235] "TBX20_(+)" "TBX3_(+)" "TBX6_(+)"
## [238] "TCF4_(+)" "TCF7_(+)" "TET1_(+)"
## [241] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)"
## [244] "TFEB_(+)" "THAP1_(+)" "TLX2_(+)"
## [247] "TLX3_(+)" "TRPS1_(+)" "UQCRB_(+)"
## [250] "USF2_(+)" "VEZF1_(+)" "VSX1_(+)"
## [253] "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [256] "ZBTB41_(+)" "ZBTB43_(+)" "ZEB1_(+)"
## [259] "ZFHX2_(+)" "ZIC2_(+)" "ZNF160_(+)"
## [262] "ZNF189_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [265] "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)"
## [268] "ZNF281_(+)" "ZNF316_(+)" "ZNF441_(+)"
## [271] "ZNF442_(+)" "ZNF467_(+)" "ZNF471_(+)"
## [274] "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [277] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)"
## [280] "ZNF668_(+)" "ZNF713_(+)" "ZNF721_(+)"
## [283] "ZNF740_(+)" "ZNF816_(+)" "ZNF836_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $IAVdNS1_infected_NHBE
## [1] "AIRE_(+)" "ALX1_(+)" "AR_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [6] "ATF1_(+)" "ATF3_(+)" "ATF5_(+)" "BACH2_(+)" "BATF_(+)"
## [11] "BCL3_(+)" "BCLAF1_(+)" "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [16] "BNC2_(+)" "BRF1_(+)" "CCNT2_(+)" "CDX2_(+)" "CEBPA_(+)"
## [21] "CEBPB_(+)" "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)" "CKMT1B_(+)"
## [26] "CNOT3_(+)" "CPSF4_(+)" "CREB1_(+)" "CREB3_(+)" "CREB3L1_(+)"
## [31] "CTCF_(+)" "DBX1_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F3_(+)"
## [36] "E2F4_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)" "EGR2_(+)"
## [41] "EGR3_(+)" "ELK3_(+)" "EMX1_(+)" "EN2_(+)" "ENO1_(+)"
## [46] "EP300_(+)" "ERF_(+)" "ESR2_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [51] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)" "EVX2_(+)" "FGF19_(+)"
## [56] "FOS_(+)" "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)" "FOXB1_(+)"
## [61] "FOXC1_(+)" "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [66] "FOXD4L4_(+)" "FOXD4L6_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [71] "FOXO1_(+)" "FOXO3_(+)" "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [76] "GATA6_(+)" "GCM1_(+)" "GMEB1_(+)" "GMEB2_(+)" "GPD1_(+)"
## [81] "GRHL2_(+)" "GSX1_(+)" "GTF2IRD1_(+)" "HAND1_(+)" "HDAC1_(+)"
## [86] "HES5_(+)" "HIC1_(+)" "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [91] "HNF1B_(+)" "HOXA10_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [96] "HOXB13_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [101] "HOXC10_(+)" "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)" "HOXC8_(+)"
## [106] "HOXC9_(+)" "HOXD11_(+)" "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [111] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)" "IKZF3_(+)" "ING3_(+)"
## [116] "IRF1_(+)" "IRF4_(+)" "IRX2_(+)" "IRX5_(+)" "ISL2_(+)"
## [121] "JUN_(+)" "JUNB_(+)" "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [126] "KLF11_(+)" "KLF12_(+)" "KLF14_(+)" "KLF2_(+)" "KLF5_(+)"
## [131] "KLF8_(+)" "LHX4_(+)" "LHX8_(+)" "LHX9_(+)" "MAF_(+)"
## [136] "MAFB_(+)" "MAFF_(+)" "MAFG_(+)" "MEF2B_(+)" "MLXIP_(+)"
## [141] "MLXIPL_(+)" "MNT_(+)" "MNX1_(+)" "MSX1_(+)" "MSX2_(+)"
## [146] "MXD4_(+)" "MXI1_(+)" "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [151] "MZF1_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)" "NFIA_(+)"
## [156] "NFIB_(+)" "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)" "NHLH1_(+)"
## [161] "NHLH2_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [166] "NR1D1_(+)" "NR2C1_(+)" "NR2F1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [171] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)" "ONECUT2_(+)" "ONECUT3_(+)"
## [176] "OTP_(+)" "PATZ1_(+)" "PAX7_(+)" "PHF21A_(+)" "PKNOX1_(+)"
## [181] "POLE3_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU1F1_(+)"
## [186] "POU3F2_(+)" "POU3F4_(+)" "POU4F3_(+)" "POU5F1_(+)" "PPARD_(+)"
## [191] "PROX1_(+)" "PSMD12_(+)" "RARB_(+)" "RARG_(+)" "RBBP5_(+)"
## [196] "REL_(+)" "RELA_(+)" "RFX1_(+)" "RFX2_(+)" "RFX3_(+)"
## [201] "RFX5_(+)" "RFXAP_(+)" "SHOX2_(+)" "SIX4_(+)" "SIX5_(+)"
## [206] "SMAD3_(+)" "SNAPC4_(+)" "SOHLH2_(+)" "SOX1_(+)" "SOX13_(+)"
## [211] "SOX15_(+)" "SOX21_(+)" "SOX4_(+)" "SOX6_(+)" "SP9_(+)"
## [216] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)" "TAF7_(+)" "TAGLN2_(+)"
## [221] "TAL1_(+)" "TBP_(+)" "TBPL1_(+)" "TBX18_(+)" "TBX20_(+)"
## [226] "TBX3_(+)" "TCF4_(+)" "TCF7_(+)" "TEF_(+)" "TET1_(+)"
## [231] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)"
## [236] "TLX3_(+)" "TRPS1_(+)" "UBP1_(+)" "UBTF_(+)" "UQCRB_(+)"
## [241] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [246] "YY2_(+)" "ZBTB41_(+)" "ZBTB43_(+)" "ZDHHC15_(+)" "ZEB1_(+)"
## [251] "ZFHX2_(+)" "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)"
## [256] "ZNF143_(+)" "ZNF160_(+)" "ZNF205_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [261] "ZNF25_(+)" "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)" "ZNF281_(+)"
## [266] "ZNF316_(+)" "ZNF426_(+)" "ZNF441_(+)" "ZNF449_(+)" "ZNF467_(+)"
## [271] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [276] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)" "ZNF668_(+)" "ZNF713_(+)"
## [281] "ZNF717_(+)" "ZNF721_(+)" "ZNF740_(+)" "ZNF816_(+)" "ZNF841_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $RSV_infected_A549
## [1] "ARNT_(+)" "BCLAF1_(+)" "BHLHE40_(+)" "CDX1_(+)" "CLOCK_(+)"
## [6] "CREB5_(+)" "ELF2_(+)" "ELK3_(+)" "EP300_(+)" "ETV1_(+)"
## [11] "ETV3_(+)" "FOSL2_(+)" "GMEB1_(+)" "HEY1_(+)" "HOXB6_(+)"
## [16] "IRX2_(+)" "KLF7_(+)" "MAX_(+)" "MNX1_(+)" "MXD3_(+)"
## [21] "MYCN_(+)" "NFATC2_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)"
## [26] "NKX3-1_(+)" "NR2F1_(+)" "PKNOX1_(+)" "POLR3A_(+)" "POLR3G_(+)"
## [31] "PPARD_(+)" "PRDM16_(+)" "REL_(+)" "RREB1_(+)" "SMAD1_(+)"
## [36] "SNAI3_(+)" "SP5_(+)" "TCF7_(+)" "ZFX_(+)" "ZNF208_(+)"
## [41] "ZNF264_(+)" "ZNF267_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF502_(+)"
## [46] "ZNF560_(+)" "ZNF773_(+)"
##
## $SARSCoV2_infected_A549
## [1] "ALX1_(+)" "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)"
## [6] "ARNTL2_(+)" "ATF2_(+)" "ATF4_(+)" "ATF6_(+)" "BACH1_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHA15_(+)"
## [16] "BHLHE40_(+)" "BRF1_(+)" "CDX2_(+)" "CELF6_(+)" "CLOCK_(+)"
## [21] "CPEB1_(+)" "CTCFL_(+)" "DLX3_(+)" "DLX4_(+)" "DLX5_(+)"
## [26] "DRGX_(+)" "E2F1_(+)" "E2F2_(+)" "E2F4_(+)" "E2F5_(+)"
## [31] "EHF_(+)" "ELF1_(+)" "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [36] "EN1_(+)" "ERF_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)"
## [41] "ETV3_(+)" "FEV_(+)" "FLI1_(+)" "FOSL2_(+)" "FOXA3_(+)"
## [46] "FOXD2_(+)" "FOXD3_(+)" "FOXF2_(+)" "FOXP4_(+)" "FOXQ1_(+)"
## [51] "GABPA_(+)" "GABPB1_(+)" "GATA5_(+)" "GCM1_(+)" "GLI1_(+)"
## [56] "GLIS2_(+)" "GRHL3_(+)" "GRHPR_(+)" "GSX2_(+)" "GTF2B_(+)"
## [61] "GTF2IRD1_(+)" "GTF3A_(+)" "HES5_(+)" "HES6_(+)" "HEY1_(+)"
## [66] "HIC1_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)" "HOXA1_(+)"
## [71] "HOXA6_(+)" "HOXA7_(+)" "HOXB13_(+)" "HOXB2_(+)" "HOXB5_(+)"
## [76] "HOXB6_(+)" "HOXB8_(+)" "HOXC10_(+)" "HOXC11_(+)" "HOXC6_(+)"
## [81] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [86] "IKZF2_(+)" "ING3_(+)" "IRF2_(+)" "IRF6_(+)" "IRF9_(+)"
## [91] "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "JUND_(+)" "KLF10_(+)"
## [96] "KLF6_(+)" "KLF7_(+)" "KLF8_(+)" "LBX2_(+)" "LHX2_(+)"
## [101] "LMX1B_(+)" "MAF_(+)" "MAFA_(+)" "MAX_(+)" "MAZ_(+)"
## [106] "MECOM_(+)" "MEOX1_(+)" "MESP1_(+)" "MNX1_(+)" "MXD1_(+)"
## [111] "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [116] "MZF1_(+)" "NEUROD1_(+)" "NFATC4_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [121] "NFIB_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)"
## [126] "NKX2-1_(+)" "NKX2-5_(+)" "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [131] "NR2E1_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR6A1_(+)" "ONECUT2_(+)"
## [136] "OTP_(+)" "OTX1_(+)" "PATZ1_(+)" "PAX7_(+)" "PAX9_(+)"
## [141] "PHF8_(+)" "PKNOX1_(+)" "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)"
## [146] "POLR3G_(+)" "POU3F4_(+)" "PRDM1_(+)" "PRDM15_(+)" "PRRX2_(+)"
## [151] "PSMD12_(+)" "RAB18_(+)" "RB1_(+)" "RFX1_(+)" "RFX2_(+)"
## [156] "RREB1_(+)" "RUNX2_(+)" "RXRG_(+)" "SATB1_(+)" "SHOX2_(+)"
## [161] "SIN3A_(+)" "SIX5_(+)" "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [166] "SNAI1_(+)" "SNAI2_(+)" "SNAI3_(+)" "SOX5_(+)" "SP3_(+)"
## [171] "SP5_(+)" "SPDEF_(+)" "STAT1_(+)" "STAT5B_(+)" "TAL2_(+)"
## [176] "TCF3_(+)" "TCF7L1_(+)" "TCF7L2_(+)" "TEAD2_(+)" "TFAP2A_(+)"
## [181] "TFAP2C_(+)" "TFDP2_(+)" "THRA_(+)" "TLX1_(+)" "TLX2_(+)"
## [186] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VSX2_(+)"
## [191] "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)" "ZNF134_(+)"
## [196] "ZNF143_(+)" "ZNF219_(+)" "ZNF267_(+)" "ZNF281_(+)" "ZNF319_(+)"
## [201] "ZNF35_(+)" "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)"
## [206] "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)" "ZNF524_(+)"
## [211] "ZNF554_(+)" "ZNF560_(+)" "ZNF583_(+)" "ZNF597_(+)" "ZNF672_(+)"
## [216] "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)" "ZNF75A_(+)" "ZNF768_(+)"
## [221] "ZNF773_(+)" "ZNF787_(+)"
##
## $SARSCoV2_infected_A549_hACE2
## [1] "ATF3_(+)" "CEBPD_(+)" "DLX2_(+)" "EGR3_(+)" "EMX1_(+)"
## [6] "ETV6_(+)" "ETV7_(+)" "FOXK1_(+)" "HIVEP2_(+)" "HOXB6_(+)"
## [11] "IRF1_(+)" "IRF5_(+)" "IRF8_(+)" "IRF9_(+)" "KLF13_(+)"
## [16] "MEF2B_(+)" "NEUROD2_(+)" "NFE2L2_(+)" "NKX3-1_(+)" "RXRG_(+)"
## [21] "SMARCA5_(+)" "SOX2_(+)" "SOX21_(+)" "STAT1_(+)" "STAT2_(+)"
## [26] "TP53_(+)" "TP73_(+)" "XBP1_(+)" "ZNF768_(+)"
##
## $SARSCoV2_infected_A549_hACE2_pt
## [1] "AIRE_(+)" "AKR1A1_(+)" "ALX4_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF3_(+)" "BCLAF1_(+)" "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"
## [11] "CDX2_(+)" "CEBPA_(+)" "CEBPD_(+)" "CLOCK_(+)" "CTCFL_(+)"
## [16] "DLX2_(+)" "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)"
## [21] "E2F1_(+)" "E2F2_(+)" "E2F7_(+)" "E2F8_(+)" "EBF1_(+)"
## [26] "EGR1_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELK3_(+)"
## [31] "ELK4_(+)" "EMX1_(+)" "ENO1_(+)" "ERF_(+)" "ETS1_(+)"
## [36] "ETS2_(+)" "ETV6_(+)" "ETV7_(+)" "FOSB_(+)" "FOSL2_(+)"
## [41] "FOXB1_(+)" "FOXD3_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [46] "FOXN1_(+)" "FOXO1_(+)" "FOXP1_(+)" "GATA5_(+)" "GLI1_(+)"
## [51] "GRHPR_(+)" "GSC2_(+)" "GTF2B_(+)" "HES6_(+)" "HEY1_(+)"
## [56] "HIVEP2_(+)" "HLX_(+)" "HNF4G_(+)" "HOXA2_(+)" "HOXA6_(+)"
## [61] "HOXA9_(+)" "HOXB1_(+)" "HOXB6_(+)" "HOXC11_(+)" "HOXC5_(+)"
## [66] "HOXC9_(+)" "HOXD4_(+)" "HSF1_(+)" "IKZF2_(+)" "IRF1_(+)"
## [71] "IRF2_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [76] "IRF9_(+)" "IRX5_(+)" "JUND_(+)" "KDM4D_(+)" "KLF13_(+)"
## [81] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)" "LHX1_(+)" "LHX2_(+)"
## [86] "LMX1B_(+)" "MAFB_(+)" "MAX_(+)" "MAZ_(+)" "MLXIP_(+)"
## [91] "MLXIPL_(+)" "MNX1_(+)" "MXD3_(+)" "MYCN_(+)" "MYEF2_(+)"
## [96] "MZF1_(+)" "NEUROD2_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [101] "NFKB1_(+)" "NKX2-2_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR1D1_(+)"
## [106] "NR1H3_(+)" "NR1H4_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR3C2_(+)"
## [111] "NR4A1_(+)" "ONECUT2_(+)" "PBX3_(+)" "PDX1_(+)" "PHF21A_(+)"
## [116] "POLE4_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F3_(+)" "POU3F1_(+)"
## [121] "POU3F4_(+)" "PPARD_(+)" "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [126] "REL_(+)" "RFX1_(+)" "RFXAP_(+)" "RUNX2_(+)" "RXRG_(+)"
## [131] "SATB1_(+)" "SETDB1_(+)" "SHOX2_(+)" "SIX2_(+)" "SIX5_(+)"
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)" "SOX2_(+)" "SOX21_(+)"
## [141] "SOX9_(+)" "SP6_(+)" "SREBF1_(+)" "STAT1_(+)" "STAT2_(+)"
## [146] "STAT5B_(+)" "TAF1_(+)" "TBX20_(+)" "TBX3_(+)" "TCF12_(+)"
## [151] "TEAD2_(+)" "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)" "TGIF1_(+)"
## [156] "TP73_(+)" "TRIM28_(+)" "TWIST1_(+)" "USF1_(+)" "VAX1_(+)"
## [161] "VEZF1_(+)" "XBP1_(+)" "ZBED1_(+)" "ZBTB41_(+)" "ZFHX3_(+)"
## [166] "ZFX_(+)" "ZNF239_(+)" "ZNF274_(+)" "ZNF276_(+)" "ZNF460_(+)"
## [171] "ZNF502_(+)" "ZNF524_(+)" "ZNF579_(+)" "ZNF583_(+)" "ZNF652_(+)"
## [176] "ZNF668_(+)" "ZNF672_(+)" "ZNF701_(+)" "ZNF721_(+)" "ZNF730_(+)"
## [181] "ZNF768_(+)" "ZNF773_(+)" "ZNF787_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_Calu3
## [1] "AKR1A1_(+)" "ALX4_(+)" "AR_(+)"
## [4] "ARID3C_(+)" "ARID5B_(+)" "ARNT_(+)"
## [7] "ARNT2_(+)" "ARNTL_(+)" "ARNTL2_(+)"
## [10] "ARX_(+)" "ASCL1_(+)" "ASCL2_(+)"
## [13] "ATF3_(+)" "ATF4_(+)" "ATF6_(+)"
## [16] "ATF6B_(+)" "BACH2_(+)" "BATF_(+)"
## [19] "BBX_(+)" "BCL11A_(+)" "BCL3_(+)"
## [22] "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [25] "BNC2_(+)" "BORCS8-MEF2B_(+)" "BRCA1_(+)"
## [28] "BRF2_(+)" "CCNT2_(+)" "CDX2_(+)"
## [31] "CEBPD_(+)" "CEBPG_(+)" "CIC_(+)"
## [34] "CPEB1_(+)" "CREB3L1_(+)" "CREB5_(+)"
## [37] "CREBL2_(+)" "CTCF_(+)" "CUX1_(+)"
## [40] "DBP_(+)" "DDIT3_(+)" "DLX2_(+)"
## [43] "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)"
## [46] "DRGX_(+)" "DUX4_(+)" "DUXA_(+)"
## [49] "E2F1_(+)" "E2F2_(+)" "E2F8_(+)"
## [52] "E4F1_(+)" "EGR2_(+)" "EGR3_(+)"
## [55] "EHF_(+)" "ELF1_(+)" "ELF4_(+)"
## [58] "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [61] "EMX1_(+)" "ENO1_(+)" "EOMES_(+)"
## [64] "EP300_(+)" "ESRRA_(+)" "ESX1_(+)"
## [67] "ETS1_(+)" "ETS2_(+)" "ETV3_(+)"
## [70] "ETV4_(+)" "ETV6_(+)" "ETV7_(+)"
## [73] "EVX2_(+)" "FBXL19_(+)" "FEV_(+)"
## [76] "FOSB_(+)" "FOSL1_(+)" "FOSL2_(+)"
## [79] "FOXA2_(+)" "FOXA3_(+)" "FOXC1_(+)"
## [82] "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)"
## [85] "FOXD4L6_(+)" "FOXF1_(+)" "FOXF2_(+)"
## [88] "FOXG1_(+)" "FOXJ2_(+)" "FOXJ3_(+)"
## [91] "FOXK1_(+)" "FOXL1_(+)" "FOXM1_(+)"
## [94] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [97] "FOXO4_(+)" "GABPB1_(+)" "GATA2_(+)"
## [100] "GATA3_(+)" "GATA5_(+)" "GATA6_(+)"
## [103] "GBX1_(+)" "GLI1_(+)" "GLIS2_(+)"
## [106] "GMEB1_(+)" "GMEB2_(+)" "GRHL1_(+)"
## [109] "GRHL2_(+)" "GRHPR_(+)" "GSC_(+)"
## [112] "GSC2_(+)" "GTF2B_(+)" "GTF2IRD1_(+)"
## [115] "GTF3A_(+)" "HAND1_(+)" "HDAC2_(+)"
## [118] "HES1_(+)" "HES5_(+)" "HES6_(+)"
## [121] "HESX1_(+)" "HEY2_(+)" "HINFP_(+)"
## [124] "HIVEP1_(+)" "HIVEP2_(+)" "HLF_(+)"
## [127] "HLX_(+)" "HMGB1_(+)" "HNF1A_(+)"
## [130] "HOXA2_(+)" "HOXA6_(+)" "HOXA9_(+)"
## [133] "HOXB4_(+)" "HOXB6_(+)" "HOXB7_(+)"
## [136] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [139] "HOXC11_(+)" "HOXC13_(+)" "HOXC4_(+)"
## [142] "HOXC6_(+)" "HOXC8_(+)" "HOXD1_(+)"
## [145] "HOXD10_(+)" "HOXD4_(+)" "HOXD8_(+)"
## [148] "HOXD9_(+)" "HSF1_(+)" "HSF2_(+)"
## [151] "IKZF2_(+)" "ING3_(+)" "IRF1_(+)"
## [154] "IRF2_(+)" "IRF4_(+)" "IRF5_(+)"
## [157] "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [160] "IRF9_(+)" "IRX2_(+)" "ISL2_(+)"
## [163] "JUN_(+)" "JUND_(+)" "KDM4D_(+)"
## [166] "KDM5A_(+)" "KLF10_(+)" "KLF11_(+)"
## [169] "KLF12_(+)" "KLF13_(+)" "KLF14_(+)"
## [172] "KLF15_(+)" "KLF16_(+)" "KLF2_(+)"
## [175] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)"
## [178] "KLF8_(+)" "KLF9_(+)" "LBX1_(+)"
## [181] "LHX1_(+)" "LHX4_(+)" "LHX5_(+)"
## [184] "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)"
## [187] "MAFK_(+)" "MAX_(+)" "MAZ_(+)"
## [190] "MECOM_(+)" "MEF2C_(+)" "MEIS1_(+)"
## [193] "MEOX2_(+)" "MESP1_(+)" "MIOS_(+)"
## [196] "MITF_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [199] "MXI1_(+)" "MYBL1_(+)" "MYCN_(+)"
## [202] "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [205] "MZF1_(+)" "NEUROD1_(+)" "NFATC2_(+)"
## [208] "NFE2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [211] "NFE2L3_(+)" "NFIC_(+)" "NFKB1_(+)"
## [214] "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)"
## [217] "NHLH2_(+)" "NKX3-1_(+)" "NKX6-2_(+)"
## [220] "NPAS2_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [223] "NR1H2_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [226] "NR1I2_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [229] "NR2F6_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [232] "NRF1_(+)" "OLIG2_(+)" "OLIG3_(+)"
## [235] "ONECUT2_(+)" "OTP_(+)" "OVOL1_(+)"
## [238] "PAX7_(+)" "PAX8_(+)" "PAX9_(+)"
## [241] "PBX1_(+)" "PDX1_(+)" "PHF2_(+)"
## [244] "PHF21A_(+)" "PHF8_(+)" "PHOX2A_(+)"
## [247] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [250] "POLR3A_(+)" "POU2F1_(+)" "POU4F1_(+)"
## [253] "POU5F1_(+)" "POU5F1B_(+)" "POU6F1_(+)"
## [256] "PPARA_(+)" "PPARD_(+)" "PRDM1_(+)"
## [259] "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [262] "RAD21_(+)" "RARA_(+)" "RARG_(+)"
## [265] "RBBP5_(+)" "REL_(+)" "RFX7_(+)"
## [268] "RREB1_(+)" "RUNX2_(+)" "SATB1_(+)"
## [271] "SETDB1_(+)" "SHOX2_(+)" "SIN3A_(+)"
## [274] "SIX1_(+)" "SIX2_(+)" "SIX5_(+)"
## [277] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [280] "SMC3_(+)" "SNAI3_(+)" "SNAPC4_(+)"
## [283] "SOX11_(+)" "SOX13_(+)" "SOX15_(+)"
## [286] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [289] "SOX9_(+)" "SP1_(+)" "SP2_(+)"
## [292] "SP6_(+)" "SP7_(+)" "SP9_(+)"
## [295] "SPDEF_(+)" "SREBF2_(+)" "SRF_(+)"
## [298] "STAT1_(+)" "STAT2_(+)" "STAT4_(+)"
## [301] "STAT5B_(+)" "STAU2_(+)" "TAF7_(+)"
## [304] "TAL1_(+)" "TBP_(+)" "TBPL2_(+)"
## [307] "TBX15_(+)" "TBX18_(+)" "TBX20_(+)"
## [310] "TBX6_(+)" "TCF3_(+)" "TCF4_(+)"
## [313] "TCF7_(+)" "TCF7L1_(+)" "TEAD4_(+)"
## [316] "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)"
## [319] "TFDP1_(+)" "TFDP2_(+)" "TFE3_(+)"
## [322] "TFEB_(+)" "TGIF2_(+)" "THAP1_(+)"
## [325] "TLX1_(+)" "TLX2_(+)" "TP73_(+)"
## [328] "TRIM28_(+)" "UBP1_(+)" "USF1_(+)"
## [331] "VAX1_(+)" "VAX2_(+)" "VDR_(+)"
## [334] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)"
## [337] "WT1_(+)" "YBX1_(+)" "YY2_(+)"
## [340] "ZBTB33_(+)" "ZEB1_(+)" "ZFHX2_(+)"
## [343] "ZFY_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [346] "ZNF160_(+)" "ZNF208_(+)" "ZNF219_(+)"
## [349] "ZNF25_(+)" "ZNF264_(+)" "ZNF267_(+)"
## [352] "ZNF276_(+)" "ZNF316_(+)" "ZNF354C_(+)"
## [355] "ZNF384_(+)" "ZNF429_(+)" "ZNF441_(+)"
## [358] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)"
## [361] "ZNF513_(+)" "ZNF524_(+)" "ZNF550_(+)"
## [364] "ZNF554_(+)" "ZNF560_(+)" "ZNF606_(+)"
## [367] "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [370] "ZNF713_(+)" "ZNF717_(+)" "ZNF721_(+)"
## [373] "ZNF761_(+)" "ZNF768_(+)" "ZNF787_(+)"
## [376] "ZNF8_(+)" "ZSCAN31_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF1_(+)" "BATF_(+)" "BBX_(+)" "BCL3_(+)" "BCL6B_(+)"
## [11] "CEBPB_(+)" "CEBPG_(+)" "CKMT1B_(+)" "CREB1_(+)" "CREB3_(+)"
## [16] "CREBL2_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [21] "EBF1_(+)" "EGR2_(+)" "ERF_(+)" "ESRRA_(+)" "ETV1_(+)"
## [26] "ETV6_(+)" "ETV7_(+)" "FOSL1_(+)" "FOXA2_(+)" "FOXF2_(+)"
## [31] "FOXK2_(+)" "FOXP3_(+)" "FOXQ1_(+)" "GATA2_(+)" "GATA3_(+)"
## [36] "HDAC2_(+)" "HES5_(+)" "HLF_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [41] "HOXA2_(+)" "HOXA5_(+)" "HOXA7_(+)" "HOXA9_(+)" "HOXB5_(+)"
## [46] "HOXB6_(+)" "HOXB7_(+)" "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [51] "HOXC4_(+)" "HOXC5_(+)" "HOXC6_(+)" "HOXC8_(+)" "HSF2_(+)"
## [56] "ING3_(+)" "IRF1_(+)" "IRF3_(+)" "IRF4_(+)" "IRF5_(+)"
## [61] "IRF8_(+)" "IRF9_(+)" "IRX2_(+)" "ISL2_(+)" "JUN_(+)"
## [66] "KLF10_(+)" "KLF5_(+)" "LHX1_(+)" "LHX4_(+)" "LHX8_(+)"
## [71] "LHX9_(+)" "MAFF_(+)" "MEOX2_(+)" "MIOS_(+)" "MLXIP_(+)"
## [76] "MSX1_(+)" "MSX2_(+)" "MXD4_(+)" "MYEF2_(+)" "NFIL3_(+)"
## [81] "NFYB_(+)" "NHLH1_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NR1I2_(+)"
## [86] "NR4A1_(+)" "NRF1_(+)" "ONECUT2_(+)" "OVOL2_(+)" "PAX2_(+)"
## [91] "PAX7_(+)" "PBX1_(+)" "PDX1_(+)" "PKNOX1_(+)" "POU2F3_(+)"
## [96] "PRDM16_(+)" "RARG_(+)" "RBBP5_(+)" "RELA_(+)" "RFX5_(+)"
## [101] "SIX2_(+)" "SMC3_(+)" "SOX13_(+)" "SOX2_(+)" "SP1_(+)"
## [106] "SP2_(+)" "SP4_(+)" "SP7_(+)" "SREBF2_(+)" "STAT1_(+)"
## [111] "STAT2_(+)" "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBP_(+)"
## [116] "TBPL1_(+)" "TBPL2_(+)" "TBX15_(+)" "TBX3_(+)" "TCF7_(+)"
## [121] "TET1_(+)" "TFAP2A_(+)" "TFE3_(+)" "TFEB_(+)" "TLX3_(+)"
## [126] "TWIST1_(+)" "UBTF_(+)" "UQCRB_(+)" "VSX1_(+)" "WT1_(+)"
## [131] "ZEB1_(+)" "ZFHX2_(+)" "ZFY_(+)" "ZNF160_(+)" "ZNF471_(+)"
## [136] "ZNF502_(+)" "ZNF560_(+)" "ZNF580_(+)" "ZNF768_(+)" "ZNF773_(+)"
## [141] "ZXDC_(+)"
##
## $human_IFNB_treated_NHBE
## [1] "ATF3_(+)" "BACH2_(+)" "ELF3_(+)" "ETV6_(+)" "ETV7_(+)"
## [6] "FOXA1_(+)" "FOXK1_(+)" "GATA2_(+)" "GCM1_(+)" "GTF2B_(+)"
## [11] "HIVEP2_(+)" "HLX_(+)" "HOXD11_(+)" "IRF1_(+)" "IRF2_(+)"
## [16] "IRF7_(+)" "IRF8_(+)" "IRF9_(+)" "NFIL3_(+)" "NFIX_(+)"
## [21] "NKX3-1_(+)" "POU5F1B_(+)" "PRDM16_(+)" "RARA_(+)" "RELA_(+)"
## [26] "RXRB_(+)" "SOX11_(+)" "SOX9_(+)" "STAT2_(+)" "TFEB_(+)"
## [31] "VEZF1_(+)"tfs_da_down## $HPIV3_infected_A549
## [1] "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNTL_(+)" "ATF1_(+)"
## [6] "ATF4_(+)" "ATF5_(+)" "BCL6B_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [11] "BRF1_(+)" "CDX1_(+)" "CHD2_(+)" "CLOCK_(+)" "CPEB1_(+)"
## [16] "CREB1_(+)" "CREB5_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F1_(+)"
## [21] "E4F1_(+)" "ELF2_(+)" "ESRRA_(+)" "FOSL1_(+)" "FOXA2_(+)"
## [26] "FOXB1_(+)" "FOXC2_(+)" "FOXF2_(+)" "FOXK1_(+)" "FOXO1_(+)"
## [31] "FOXO3_(+)" "FOXP2_(+)" "GABPB1_(+)" "GCM1_(+)" "HAND1_(+)"
## [36] "HES6_(+)" "HEY1_(+)" "HEY2_(+)" "HIVEP2_(+)" "HLF_(+)"
## [41] "HOXA9_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [46] "HOXC10_(+)" "HOXC13_(+)" "HOXC8_(+)" "HOXD11_(+)" "HSF2_(+)"
## [51] "IKZF2_(+)" "IRF4_(+)" "ISL2_(+)" "KDM5A_(+)" "KLF3_(+)"
## [56] "KLF7_(+)" "KLF9_(+)" "LHX4_(+)" "MAF_(+)" "MAZ_(+)"
## [61] "MECOM_(+)" "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)"
## [66] "NEUROD1_(+)" "NFE2L1_(+)" "NFIA_(+)" "NFIL3_(+)" "NFKB1_(+)"
## [71] "NFKB2_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)" "NKX3-1_(+)"
## [76] "NR2C1_(+)" "NR5A2_(+)" "OTP_(+)" "PAX7_(+)" "POU3F2_(+)"
## [81] "POU5F1_(+)" "RARB_(+)" "RFX2_(+)" "RFX3_(+)" "RREB1_(+)"
## [86] "RUNX2_(+)" "SNAI3_(+)" "SOX1_(+)" "SOX15_(+)" "SP6_(+)"
## [91] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBX15_(+)" "TBX20_(+)"
## [96] "TCF3_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)" "VSX1_(+)"
## [101] "ZBTB33_(+)" "ZBTB7A_(+)" "ZEB1_(+)" "ZFX_(+)" "ZIC2_(+)"
## [106] "ZNF134_(+)" "ZNF143_(+)" "ZNF148_(+)" "ZNF160_(+)" "ZNF227_(+)"
## [111] "ZNF354C_(+)" "ZNF429_(+)" "ZNF449_(+)" "ZNF502_(+)" "ZNF524_(+)"
## [116] "ZNF571_(+)" "ZNF597_(+)" "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [121] "ZNF787_(+)" "ZNF841_(+)" "ZSCAN26_(+)"
##
## $IAV_infected_A549
## [1] "ALX1_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)" "ARNTL2_(+)"
## [6] "ASCL2_(+)" "ATF2_(+)" "ATF4_(+)" "BACH1_(+)" "BATF_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHE40_(+)"
## [16] "BRF1_(+)" "CDX2_(+)" "CLOCK_(+)" "CPEB1_(+)" "CREB5_(+)"
## [21] "CTCFL_(+)" "DLX3_(+)" "DLX5_(+)" "E2F1_(+)" "E2F2_(+)"
## [26] "E2F4_(+)" "E2F5_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)"
## [31] "EGR3_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELF5_(+)"
## [36] "ELK3_(+)" "ELK4_(+)" "EN1_(+)" "EN2_(+)" "ERF_(+)"
## [41] "ESRRA_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)" "ETV7_(+)"
## [46] "FOSB_(+)" "FOSL2_(+)" "FOXB1_(+)" "FOXC1_(+)" "FOXD3_(+)"
## [51] "FOXF2_(+)" "FOXM1_(+)" "FOXO1_(+)" "GABPA_(+)" "GABPB1_(+)"
## [56] "GATA5_(+)" "GCM1_(+)" "GLI1_(+)" "GLIS2_(+)" "GRHL1_(+)"
## [61] "GRHL3_(+)" "GRHPR_(+)" "GSC_(+)" "GSX2_(+)" "GTF2B_(+)"
## [66] "GTF2IRD1_(+)" "HES1_(+)" "HES5_(+)" "HES6_(+)" "HIC1_(+)"
## [71] "HINFP_(+)" "HIVEP2_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [76] "HOXA1_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA6_(+)" "HOXA7_(+)"
## [81] "HOXA9_(+)" "HOXB13_(+)" "HOXB5_(+)" "HOXB7_(+)" "HOXB8_(+)"
## [86] "HOXC10_(+)" "HOXC11_(+)" "HOXC13_(+)" "HOXC5_(+)" "HOXC6_(+)"
## [91] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HTATIP2_(+)" "IRF1_(+)"
## [96] "IRF2_(+)" "IRF3_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)"
## [101] "IRF9_(+)" "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "IRX5_(+)"
## [106] "JUND_(+)" "KLF10_(+)" "KLF3_(+)" "KLF4_(+)" "KLF5_(+)"
## [111] "KLF6_(+)" "KLF8_(+)" "KLF9_(+)" "LBX2_(+)" "LHX2_(+)"
## [116] "LHX5_(+)" "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)" "MAFG_(+)"
## [121] "MAX_(+)" "MAZ_(+)" "MECOM_(+)" "MEOX1_(+)" "MNX1_(+)"
## [126] "MSX2_(+)" "MTF1_(+)" "MXD1_(+)" "MXD3_(+)" "MXD4_(+)"
## [131] "MXI1_(+)" "MYCN_(+)" "MYEF2_(+)" "MYPOP_(+)" "MZF1_(+)"
## [136] "NEUROD1_(+)" "NFATC4_(+)" "NFE2_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [141] "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)" "NKX2-1_(+)"
## [146] "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [151] "NR2F6_(+)" "ONECUT2_(+)" "OTP_(+)" "OTX1_(+)" "OVOL2_(+)"
## [156] "PAX7_(+)" "PAX9_(+)" "PHF21A_(+)" "PHF8_(+)" "PKNOX1_(+)"
## [161] "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F1_(+)"
## [166] "POU2F3_(+)" "POU3F1_(+)" "POU3F4_(+)" "PPARD_(+)" "PRDM1_(+)"
## [171] "PRDM15_(+)" "PRRX2_(+)" "PSMD12_(+)" "RAB18_(+)" "RARG_(+)"
## [176] "REL_(+)" "RFX2_(+)" "RORA_(+)" "RREB1_(+)" "RXRG_(+)"
## [181] "SATB1_(+)" "SETDB1_(+)" "SIN3A_(+)" "SIX2_(+)" "SIX5_(+)"
## [186] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)" "SNAI2_(+)" "SNAI3_(+)"
## [191] "SOX5_(+)" "SP3_(+)" "SP5_(+)" "STAT1_(+)" "STAT2_(+)"
## [196] "STAT5A_(+)" "STAT5B_(+)" "TAGLN2_(+)" "TBPL2_(+)" "TCF12_(+)"
## [201] "TCF3_(+)" "TCF7_(+)" "TEAD4_(+)" "TEF_(+)" "TFAP2A_(+)"
## [206] "TFAP2C_(+)" "TFAP2E_(+)" "TFDP2_(+)" "TGIF2_(+)" "TLX2_(+)"
## [211] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VDR_(+)"
## [216] "VSX2_(+)" "ZBTB7A_(+)" "ZFX_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [221] "ZNF208_(+)" "ZNF219_(+)" "ZNF274_(+)" "ZNF281_(+)" "ZNF35_(+)"
## [226] "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)" "ZNF483_(+)"
## [231] "ZNF502_(+)" "ZNF524_(+)" "ZNF554_(+)" "ZNF560_(+)" "ZNF597_(+)"
## [236] "ZNF672_(+)" "ZNF682_(+)" "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)"
## [241] "ZNF761_(+)" "ZNF773_(+)" "ZNF787_(+)"
##
## $IAV_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)"
## [4] "ALX3_(+)" "ALX4_(+)" "AR_(+)"
## [7] "ARID5B_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [10] "ATF1_(+)" "ATF3_(+)" "BACH2_(+)"
## [13] "BATF_(+)" "BCL3_(+)" "BCLAF1_(+)"
## [16] "BDP1_(+)" "BHLHE41_(+)" "BNC2_(+)"
## [19] "BORCS8-MEF2B_(+)" "BRF1_(+)" "CCNT2_(+)"
## [22] "CDX2_(+)" "CEBPA_(+)" "CEBPB_(+)"
## [25] "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)"
## [28] "CKMT1B_(+)" "CLOCK_(+)" "CNOT3_(+)"
## [31] "CPEB1_(+)" "CPSF4_(+)" "CREB1_(+)"
## [34] "CREB3_(+)" "CREB3L1_(+)" "CUX1_(+)"
## [37] "DBX1_(+)" "DLX2_(+)" "DLX4_(+)"
## [40] "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [43] "E2F3_(+)" "E2F4_(+)" "E2F6_(+)"
## [46] "EGR1_(+)" "EGR2_(+)" "EGR3_(+)"
## [49] "ELK3_(+)" "EMX1_(+)" "EN1_(+)"
## [52] "EN2_(+)" "ENO1_(+)" "EP300_(+)"
## [55] "ERF_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [58] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)"
## [61] "EVX2_(+)" "FGF19_(+)" "FOS_(+)"
## [64] "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)"
## [67] "FOXB1_(+)" "FOXC1_(+)" "FOXC2_(+)"
## [70] "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [73] "FOXD4L6_(+)" "FOXF2_(+)" "FOXJ2_(+)"
## [76] "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [79] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [82] "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [85] "GCM1_(+)" "GLIS2_(+)" "GMEB1_(+)"
## [88] "GRHL2_(+)" "GTF2IRD1_(+)" "HAND1_(+)"
## [91] "HDAC1_(+)" "HES5_(+)" "HEY1_(+)"
## [94] "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [97] "HNF1A_(+)" "HNF1B_(+)" "HOXA10_(+)"
## [100] "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [103] "HOXB13_(+)" "HOXB4_(+)" "HOXB6_(+)"
## [106] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [109] "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)"
## [112] "HOXC8_(+)" "HOXC9_(+)" "HOXD11_(+)"
## [115] "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [118] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [121] "IKZF3_(+)" "ING3_(+)" "IRF1_(+)"
## [124] "IRF4_(+)" "IRX2_(+)" "IRX5_(+)"
## [127] "ISL2_(+)" "JUN_(+)" "JUNB_(+)"
## [130] "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [133] "KLF10_(+)" "KLF11_(+)" "KLF12_(+)"
## [136] "KLF13_(+)" "KLF14_(+)" "KLF2_(+)"
## [139] "KLF5_(+)" "KLF8_(+)" "LHX4_(+)"
## [142] "LHX8_(+)" "LHX9_(+)" "LMX1B_(+)"
## [145] "MAF_(+)" "MAFB_(+)" "MAFF_(+)"
## [148] "MAFG_(+)" "MEF2B_(+)" "MEF2C_(+)"
## [151] "MEOX2_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [154] "MNT_(+)" "MNX1_(+)" "MSX1_(+)"
## [157] "MSX2_(+)" "MYEF2_(+)" "MYOD1_(+)"
## [160] "MZF1_(+)" "NFATC2_(+)" "NFE2L2_(+)"
## [163] "NFE2L3_(+)" "NFIA_(+)" "NFIB_(+)"
## [166] "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)"
## [169] "NHLH1_(+)" "NKX2-1_(+)" "NKX2-5_(+)"
## [172] "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [175] "NR1D1_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [178] "NR3C1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [181] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)"
## [184] "ONECUT2_(+)" "ONECUT3_(+)" "OTP_(+)"
## [187] "PATZ1_(+)" "PAX7_(+)" "PDX1_(+)"
## [190] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [193] "POLR3G_(+)" "POU3F2_(+)" "POU3F4_(+)"
## [196] "POU5F1_(+)" "PPARD_(+)" "PROX1_(+)"
## [199] "PRRX1_(+)" "PSMD12_(+)" "RARB_(+)"
## [202] "RARG_(+)" "RBBP5_(+)" "REL_(+)"
## [205] "RELA_(+)" "RFX1_(+)" "RFX2_(+)"
## [208] "RFX3_(+)" "RFX5_(+)" "RFXAP_(+)"
## [211] "SATB1_(+)" "SIN3A_(+)" "SIX2_(+)"
## [214] "SIX4_(+)" "SIX5_(+)" "SOHLH2_(+)"
## [217] "SOX1_(+)" "SOX13_(+)" "SOX15_(+)"
## [220] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [223] "SOX6_(+)" "SP7_(+)" "SP9_(+)"
## [226] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)"
## [229] "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)"
## [232] "TBP_(+)" "TBPL1_(+)" "TBX15_(+)"
## [235] "TBX20_(+)" "TBX3_(+)" "TBX6_(+)"
## [238] "TCF4_(+)" "TCF7_(+)" "TET1_(+)"
## [241] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)"
## [244] "TFEB_(+)" "THAP1_(+)" "TLX2_(+)"
## [247] "TLX3_(+)" "TRPS1_(+)" "UQCRB_(+)"
## [250] "USF2_(+)" "VEZF1_(+)" "VSX1_(+)"
## [253] "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [256] "ZBTB41_(+)" "ZBTB43_(+)" "ZEB1_(+)"
## [259] "ZFHX2_(+)" "ZIC2_(+)" "ZNF160_(+)"
## [262] "ZNF189_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [265] "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)"
## [268] "ZNF281_(+)" "ZNF316_(+)" "ZNF441_(+)"
## [271] "ZNF442_(+)" "ZNF467_(+)" "ZNF471_(+)"
## [274] "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [277] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)"
## [280] "ZNF668_(+)" "ZNF713_(+)" "ZNF721_(+)"
## [283] "ZNF740_(+)" "ZNF816_(+)" "ZNF836_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $IAVdNS1_infected_NHBE
## [1] "AIRE_(+)" "ALX1_(+)" "AR_(+)" "ARNT_(+)" "ARNTL2_(+)"
## [6] "ATF1_(+)" "ATF3_(+)" "ATF5_(+)" "BACH2_(+)" "BATF_(+)"
## [11] "BCL3_(+)" "BCLAF1_(+)" "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [16] "BNC2_(+)" "BRF1_(+)" "CCNT2_(+)" "CDX2_(+)" "CEBPA_(+)"
## [21] "CEBPB_(+)" "CEBPD_(+)" "CELF6_(+)" "CHD2_(+)" "CKMT1B_(+)"
## [26] "CNOT3_(+)" "CPSF4_(+)" "CREB1_(+)" "CREB3_(+)" "CREB3L1_(+)"
## [31] "CTCF_(+)" "DBX1_(+)" "DDIT3_(+)" "DLX2_(+)" "E2F3_(+)"
## [36] "E2F4_(+)" "E2F6_(+)" "E2F8_(+)" "EGR1_(+)" "EGR2_(+)"
## [41] "EGR3_(+)" "ELK3_(+)" "EMX1_(+)" "EN2_(+)" "ENO1_(+)"
## [46] "EP300_(+)" "ERF_(+)" "ESR2_(+)" "ESRRA_(+)" "ESRRB_(+)"
## [51] "ETV1_(+)" "ETV3_(+)" "ETV5_(+)" "EVX2_(+)" "FGF19_(+)"
## [56] "FOS_(+)" "FOSL1_(+)" "FOXA1_(+)" "FOXA2_(+)" "FOXB1_(+)"
## [61] "FOXC1_(+)" "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)" "FOXD4_(+)"
## [66] "FOXD4L4_(+)" "FOXD4L6_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [71] "FOXO1_(+)" "FOXO3_(+)" "FOXO6_(+)" "FOXQ1_(+)" "GATA3_(+)"
## [76] "GATA6_(+)" "GCM1_(+)" "GMEB1_(+)" "GMEB2_(+)" "GPD1_(+)"
## [81] "GRHL2_(+)" "GSX1_(+)" "GTF2IRD1_(+)" "HAND1_(+)" "HDAC1_(+)"
## [86] "HES5_(+)" "HIC1_(+)" "HINFP_(+)" "HLF_(+)" "HMGB1_(+)"
## [91] "HNF1B_(+)" "HOXA10_(+)" "HOXA2_(+)" "HOXA5_(+)" "HOXA9_(+)"
## [96] "HOXB13_(+)" "HOXB2_(+)" "HOXB6_(+)" "HOXB8_(+)" "HOXB9_(+)"
## [101] "HOXC10_(+)" "HOXC13_(+)" "HOXC4_(+)" "HOXC6_(+)" "HOXC8_(+)"
## [106] "HOXC9_(+)" "HOXD11_(+)" "HOXD13_(+)" "HOXD3_(+)" "HOXD4_(+)"
## [111] "HSF2_(+)" "HSF4_(+)" "HTATIP2_(+)" "IKZF3_(+)" "ING3_(+)"
## [116] "IRF1_(+)" "IRF4_(+)" "IRX2_(+)" "IRX5_(+)" "ISL2_(+)"
## [121] "JUN_(+)" "JUNB_(+)" "JUND_(+)" "KDM5A_(+)" "KLF1_(+)"
## [126] "KLF11_(+)" "KLF12_(+)" "KLF14_(+)" "KLF2_(+)" "KLF5_(+)"
## [131] "KLF8_(+)" "LHX4_(+)" "LHX8_(+)" "LHX9_(+)" "MAF_(+)"
## [136] "MAFB_(+)" "MAFF_(+)" "MAFG_(+)" "MEF2B_(+)" "MLXIP_(+)"
## [141] "MLXIPL_(+)" "MNT_(+)" "MNX1_(+)" "MSX1_(+)" "MSX2_(+)"
## [146] "MXD4_(+)" "MXI1_(+)" "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [151] "MZF1_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)" "NFIA_(+)"
## [156] "NFIB_(+)" "NFIC_(+)" "NFIL3_(+)" "NFKB2_(+)" "NHLH1_(+)"
## [161] "NHLH2_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [166] "NR1D1_(+)" "NR2C1_(+)" "NR2F1_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [171] "NR6A1_(+)" "NRF1_(+)" "ONECUT1_(+)" "ONECUT2_(+)" "ONECUT3_(+)"
## [176] "OTP_(+)" "PATZ1_(+)" "PAX7_(+)" "PHF21A_(+)" "PKNOX1_(+)"
## [181] "POLE3_(+)" "POLR2A_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU1F1_(+)"
## [186] "POU3F2_(+)" "POU3F4_(+)" "POU4F3_(+)" "POU5F1_(+)" "PPARD_(+)"
## [191] "PROX1_(+)" "PSMD12_(+)" "RARB_(+)" "RARG_(+)" "RBBP5_(+)"
## [196] "REL_(+)" "RELA_(+)" "RFX1_(+)" "RFX2_(+)" "RFX3_(+)"
## [201] "RFX5_(+)" "RFXAP_(+)" "SHOX2_(+)" "SIX4_(+)" "SIX5_(+)"
## [206] "SMAD3_(+)" "SNAPC4_(+)" "SOHLH2_(+)" "SOX1_(+)" "SOX13_(+)"
## [211] "SOX15_(+)" "SOX21_(+)" "SOX4_(+)" "SOX6_(+)" "SP9_(+)"
## [216] "SPDEF_(+)" "SREBF2_(+)" "STAT4_(+)" "TAF7_(+)" "TAGLN2_(+)"
## [221] "TAL1_(+)" "TBP_(+)" "TBPL1_(+)" "TBX18_(+)" "TBX20_(+)"
## [226] "TBX3_(+)" "TCF4_(+)" "TCF7_(+)" "TEF_(+)" "TET1_(+)"
## [231] "TFAP2A_(+)" "TFDP1_(+)" "TFE3_(+)" "TFEB_(+)" "THAP1_(+)"
## [236] "TLX3_(+)" "TRPS1_(+)" "UBP1_(+)" "UBTF_(+)" "UQCRB_(+)"
## [241] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)" "XBP1_(+)" "YBX1_(+)"
## [246] "YY2_(+)" "ZBTB41_(+)" "ZBTB43_(+)" "ZDHHC15_(+)" "ZEB1_(+)"
## [251] "ZFHX2_(+)" "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)"
## [256] "ZNF143_(+)" "ZNF160_(+)" "ZNF205_(+)" "ZNF208_(+)" "ZNF239_(+)"
## [261] "ZNF25_(+)" "ZNF263_(+)" "ZNF264_(+)" "ZNF274_(+)" "ZNF281_(+)"
## [266] "ZNF316_(+)" "ZNF426_(+)" "ZNF441_(+)" "ZNF449_(+)" "ZNF467_(+)"
## [271] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)"
## [276] "ZNF560_(+)" "ZNF571_(+)" "ZNF597_(+)" "ZNF668_(+)" "ZNF713_(+)"
## [281] "ZNF717_(+)" "ZNF721_(+)" "ZNF740_(+)" "ZNF816_(+)" "ZNF841_(+)"
## [286] "ZSCAN31_(+)" "ZXDC_(+)"
##
## $RSV_infected_A549
## [1] "ARNT_(+)" "BCLAF1_(+)" "BHLHE40_(+)" "CDX1_(+)" "CLOCK_(+)"
## [6] "CREB5_(+)" "ELF2_(+)" "ELK3_(+)" "EP300_(+)" "ETV1_(+)"
## [11] "ETV3_(+)" "FOSL2_(+)" "GMEB1_(+)" "HEY1_(+)" "HOXB6_(+)"
## [16] "IRX2_(+)" "KLF7_(+)" "MAX_(+)" "MNX1_(+)" "MXD3_(+)"
## [21] "MYCN_(+)" "NFATC2_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)"
## [26] "NKX3-1_(+)" "NR2F1_(+)" "PKNOX1_(+)" "POLR3A_(+)" "POLR3G_(+)"
## [31] "PPARD_(+)" "PRDM16_(+)" "REL_(+)" "RREB1_(+)" "SMAD1_(+)"
## [36] "SNAI3_(+)" "SP5_(+)" "TCF7_(+)" "ZFX_(+)" "ZNF208_(+)"
## [41] "ZNF264_(+)" "ZNF267_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF502_(+)"
## [46] "ZNF560_(+)" "ZNF773_(+)"
##
## $SARSCoV2_infected_A549
## [1] "ALX1_(+)" "ALX3_(+)" "ALX4_(+)" "ARNT_(+)" "ARNT2_(+)"
## [6] "ARNTL2_(+)" "ATF2_(+)" "ATF4_(+)" "ATF6_(+)" "BACH1_(+)"
## [11] "BBX_(+)" "BCL11A_(+)" "BCL11B_(+)" "BCLAF1_(+)" "BHLHA15_(+)"
## [16] "BHLHE40_(+)" "BRF1_(+)" "CDX2_(+)" "CELF6_(+)" "CLOCK_(+)"
## [21] "CPEB1_(+)" "CTCFL_(+)" "DLX3_(+)" "DLX4_(+)" "DLX5_(+)"
## [26] "DRGX_(+)" "E2F1_(+)" "E2F2_(+)" "E2F4_(+)" "E2F5_(+)"
## [31] "EHF_(+)" "ELF1_(+)" "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [36] "EN1_(+)" "ERF_(+)" "ETS1_(+)" "ETS2_(+)" "ETV1_(+)"
## [41] "ETV3_(+)" "FEV_(+)" "FLI1_(+)" "FOSL2_(+)" "FOXA3_(+)"
## [46] "FOXD2_(+)" "FOXD3_(+)" "FOXF2_(+)" "FOXP4_(+)" "FOXQ1_(+)"
## [51] "GABPA_(+)" "GABPB1_(+)" "GATA5_(+)" "GCM1_(+)" "GLI1_(+)"
## [56] "GLIS2_(+)" "GRHL3_(+)" "GRHPR_(+)" "GSX2_(+)" "GTF2B_(+)"
## [61] "GTF2IRD1_(+)" "GTF3A_(+)" "HES5_(+)" "HES6_(+)" "HEY1_(+)"
## [66] "HIC1_(+)" "HLX_(+)" "HNF1A_(+)" "HNF1B_(+)" "HOXA1_(+)"
## [71] "HOXA6_(+)" "HOXA7_(+)" "HOXB13_(+)" "HOXB2_(+)" "HOXB5_(+)"
## [76] "HOXB6_(+)" "HOXB8_(+)" "HOXC10_(+)" "HOXC11_(+)" "HOXC6_(+)"
## [81] "HOXD3_(+)" "HOXD4_(+)" "HOXD9_(+)" "HSF4_(+)" "HTATIP2_(+)"
## [86] "IKZF2_(+)" "ING3_(+)" "IRF2_(+)" "IRF6_(+)" "IRF9_(+)"
## [91] "IRX1_(+)" "IRX2_(+)" "IRX4_(+)" "JUND_(+)" "KLF10_(+)"
## [96] "KLF6_(+)" "KLF7_(+)" "KLF8_(+)" "LBX2_(+)" "LHX2_(+)"
## [101] "LMX1B_(+)" "MAF_(+)" "MAFA_(+)" "MAX_(+)" "MAZ_(+)"
## [106] "MECOM_(+)" "MEOX1_(+)" "MESP1_(+)" "MNX1_(+)" "MXD1_(+)"
## [111] "MXD3_(+)" "MXI1_(+)" "MYCN_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [116] "MZF1_(+)" "NEUROD1_(+)" "NFATC4_(+)" "NFE2L1_(+)" "NFIA_(+)"
## [121] "NFIB_(+)" "NFKB1_(+)" "NFYA_(+)" "NFYC_(+)" "NHLH2_(+)"
## [126] "NKX2-1_(+)" "NKX2-5_(+)" "NKX3-1_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [131] "NR2E1_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR6A1_(+)" "ONECUT2_(+)"
## [136] "OTP_(+)" "OTX1_(+)" "PATZ1_(+)" "PAX7_(+)" "PAX9_(+)"
## [141] "PHF8_(+)" "PKNOX1_(+)" "POLE4_(+)" "POLR2A_(+)" "POLR3A_(+)"
## [146] "POLR3G_(+)" "POU3F4_(+)" "PRDM1_(+)" "PRDM15_(+)" "PRRX2_(+)"
## [151] "PSMD12_(+)" "RAB18_(+)" "RB1_(+)" "RFX1_(+)" "RFX2_(+)"
## [156] "RREB1_(+)" "RUNX2_(+)" "RXRG_(+)" "SATB1_(+)" "SHOX2_(+)"
## [161] "SIN3A_(+)" "SIX5_(+)" "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [166] "SNAI1_(+)" "SNAI2_(+)" "SNAI3_(+)" "SOX5_(+)" "SP3_(+)"
## [171] "SP5_(+)" "SPDEF_(+)" "STAT1_(+)" "STAT5B_(+)" "TAL2_(+)"
## [176] "TCF3_(+)" "TCF7L1_(+)" "TCF7L2_(+)" "TEAD2_(+)" "TFAP2A_(+)"
## [181] "TFAP2C_(+)" "TFDP2_(+)" "THRA_(+)" "TLX1_(+)" "TLX2_(+)"
## [186] "TRIM28_(+)" "USF1_(+)" "USF2_(+)" "VAX1_(+)" "VSX2_(+)"
## [191] "ZFHX3_(+)" "ZFP64_(+)" "ZFX_(+)" "ZIC2_(+)" "ZNF134_(+)"
## [196] "ZNF143_(+)" "ZNF219_(+)" "ZNF267_(+)" "ZNF281_(+)" "ZNF319_(+)"
## [201] "ZNF35_(+)" "ZNF354C_(+)" "ZNF426_(+)" "ZNF429_(+)" "ZNF471_(+)"
## [206] "ZNF483_(+)" "ZNF486_(+)" "ZNF502_(+)" "ZNF513_(+)" "ZNF524_(+)"
## [211] "ZNF554_(+)" "ZNF560_(+)" "ZNF583_(+)" "ZNF597_(+)" "ZNF672_(+)"
## [216] "ZNF720_(+)" "ZNF729_(+)" "ZNF730_(+)" "ZNF75A_(+)" "ZNF768_(+)"
## [221] "ZNF773_(+)" "ZNF787_(+)"
##
## $SARSCoV2_infected_A549_hACE2
## [1] "ATF3_(+)" "CEBPD_(+)" "DLX2_(+)" "EGR3_(+)" "EMX1_(+)"
## [6] "ETV6_(+)" "ETV7_(+)" "FOXK1_(+)" "HIVEP2_(+)" "HOXB6_(+)"
## [11] "IRF1_(+)" "IRF5_(+)" "IRF8_(+)" "IRF9_(+)" "KLF13_(+)"
## [16] "MEF2B_(+)" "NEUROD2_(+)" "NFE2L2_(+)" "NKX3-1_(+)" "RXRG_(+)"
## [21] "SMARCA5_(+)" "SOX2_(+)" "SOX21_(+)" "STAT1_(+)" "STAT2_(+)"
## [26] "TP53_(+)" "TP73_(+)" "XBP1_(+)" "ZNF768_(+)"
##
## $SARSCoV2_infected_A549_hACE2_pt
## [1] "AIRE_(+)" "AKR1A1_(+)" "ALX4_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF3_(+)" "BCLAF1_(+)" "BHLHA15_(+)" "BHLHE40_(+)" "BRF2_(+)"
## [11] "CDX2_(+)" "CEBPA_(+)" "CEBPD_(+)" "CLOCK_(+)" "CTCFL_(+)"
## [16] "DLX2_(+)" "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)"
## [21] "E2F1_(+)" "E2F2_(+)" "E2F7_(+)" "E2F8_(+)" "EBF1_(+)"
## [26] "EGR1_(+)" "EHF_(+)" "ELF1_(+)" "ELF4_(+)" "ELK3_(+)"
## [31] "ELK4_(+)" "EMX1_(+)" "ENO1_(+)" "ERF_(+)" "ETS1_(+)"
## [36] "ETS2_(+)" "ETV6_(+)" "ETV7_(+)" "FOSB_(+)" "FOSL2_(+)"
## [41] "FOXB1_(+)" "FOXD3_(+)" "FOXK1_(+)" "FOXK2_(+)" "FOXM1_(+)"
## [46] "FOXN1_(+)" "FOXO1_(+)" "FOXP1_(+)" "GATA5_(+)" "GLI1_(+)"
## [51] "GRHPR_(+)" "GSC2_(+)" "GTF2B_(+)" "HES6_(+)" "HEY1_(+)"
## [56] "HIVEP2_(+)" "HLX_(+)" "HNF4G_(+)" "HOXA2_(+)" "HOXA6_(+)"
## [61] "HOXA9_(+)" "HOXB1_(+)" "HOXB6_(+)" "HOXC11_(+)" "HOXC5_(+)"
## [66] "HOXC9_(+)" "HOXD4_(+)" "HSF1_(+)" "IKZF2_(+)" "IRF1_(+)"
## [71] "IRF2_(+)" "IRF5_(+)" "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [76] "IRF9_(+)" "IRX5_(+)" "JUND_(+)" "KDM4D_(+)" "KLF13_(+)"
## [81] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)" "LHX1_(+)" "LHX2_(+)"
## [86] "LMX1B_(+)" "MAFB_(+)" "MAX_(+)" "MAZ_(+)" "MLXIP_(+)"
## [91] "MLXIPL_(+)" "MNX1_(+)" "MXD3_(+)" "MYCN_(+)" "MYEF2_(+)"
## [96] "MZF1_(+)" "NEUROD2_(+)" "NFATC2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [101] "NFKB1_(+)" "NKX2-2_(+)" "NKX3-1_(+)" "NPDC1_(+)" "NR1D1_(+)"
## [106] "NR1H3_(+)" "NR1H4_(+)" "NR2F1_(+)" "NR2F6_(+)" "NR3C2_(+)"
## [111] "NR4A1_(+)" "ONECUT2_(+)" "PBX3_(+)" "PDX1_(+)" "PHF21A_(+)"
## [116] "POLE4_(+)" "POLR3A_(+)" "POLR3G_(+)" "POU2F3_(+)" "POU3F1_(+)"
## [121] "POU3F4_(+)" "PPARD_(+)" "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [126] "REL_(+)" "RFX1_(+)" "RFXAP_(+)" "RUNX2_(+)" "RXRG_(+)"
## [131] "SATB1_(+)" "SETDB1_(+)" "SHOX2_(+)" "SIX2_(+)" "SIX5_(+)"
## [136] "SMARCA5_(+)" "SMARCC2_(+)" "SNAI3_(+)" "SOX2_(+)" "SOX21_(+)"
## [141] "SOX9_(+)" "SP6_(+)" "SREBF1_(+)" "STAT1_(+)" "STAT2_(+)"
## [146] "STAT5B_(+)" "TAF1_(+)" "TBX20_(+)" "TBX3_(+)" "TCF12_(+)"
## [151] "TEAD2_(+)" "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)" "TGIF1_(+)"
## [156] "TP73_(+)" "TRIM28_(+)" "TWIST1_(+)" "USF1_(+)" "VAX1_(+)"
## [161] "VEZF1_(+)" "XBP1_(+)" "ZBED1_(+)" "ZBTB41_(+)" "ZFHX3_(+)"
## [166] "ZFX_(+)" "ZNF239_(+)" "ZNF274_(+)" "ZNF276_(+)" "ZNF460_(+)"
## [171] "ZNF502_(+)" "ZNF524_(+)" "ZNF579_(+)" "ZNF583_(+)" "ZNF652_(+)"
## [176] "ZNF668_(+)" "ZNF672_(+)" "ZNF701_(+)" "ZNF721_(+)" "ZNF730_(+)"
## [181] "ZNF768_(+)" "ZNF773_(+)" "ZNF787_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_Calu3
## [1] "AKR1A1_(+)" "ALX4_(+)" "AR_(+)"
## [4] "ARID3C_(+)" "ARID5B_(+)" "ARNT_(+)"
## [7] "ARNT2_(+)" "ARNTL_(+)" "ARNTL2_(+)"
## [10] "ARX_(+)" "ASCL1_(+)" "ASCL2_(+)"
## [13] "ATF3_(+)" "ATF4_(+)" "ATF6_(+)"
## [16] "ATF6B_(+)" "BACH2_(+)" "BATF_(+)"
## [19] "BBX_(+)" "BCL11A_(+)" "BCL3_(+)"
## [22] "BDP1_(+)" "BHLHE40_(+)" "BHLHE41_(+)"
## [25] "BNC2_(+)" "BORCS8-MEF2B_(+)" "BRCA1_(+)"
## [28] "BRF2_(+)" "CCNT2_(+)" "CDX2_(+)"
## [31] "CEBPD_(+)" "CEBPG_(+)" "CIC_(+)"
## [34] "CPEB1_(+)" "CREB3L1_(+)" "CREB5_(+)"
## [37] "CREBL2_(+)" "CTCF_(+)" "CUX1_(+)"
## [40] "DBP_(+)" "DDIT3_(+)" "DLX2_(+)"
## [43] "DLX3_(+)" "DLX4_(+)" "DMRT1_(+)"
## [46] "DRGX_(+)" "DUX4_(+)" "DUXA_(+)"
## [49] "E2F1_(+)" "E2F2_(+)" "E2F8_(+)"
## [52] "E4F1_(+)" "EGR2_(+)" "EGR3_(+)"
## [55] "EHF_(+)" "ELF1_(+)" "ELF4_(+)"
## [58] "ELK1_(+)" "ELK3_(+)" "ELK4_(+)"
## [61] "EMX1_(+)" "ENO1_(+)" "EOMES_(+)"
## [64] "EP300_(+)" "ESRRA_(+)" "ESX1_(+)"
## [67] "ETS1_(+)" "ETS2_(+)" "ETV3_(+)"
## [70] "ETV4_(+)" "ETV6_(+)" "ETV7_(+)"
## [73] "EVX2_(+)" "FBXL19_(+)" "FEV_(+)"
## [76] "FOSB_(+)" "FOSL1_(+)" "FOSL2_(+)"
## [79] "FOXA2_(+)" "FOXA3_(+)" "FOXC1_(+)"
## [82] "FOXC2_(+)" "FOXD2_(+)" "FOXD3_(+)"
## [85] "FOXD4L6_(+)" "FOXF1_(+)" "FOXF2_(+)"
## [88] "FOXG1_(+)" "FOXJ2_(+)" "FOXJ3_(+)"
## [91] "FOXK1_(+)" "FOXL1_(+)" "FOXM1_(+)"
## [94] "FOXN1_(+)" "FOXO1_(+)" "FOXO3_(+)"
## [97] "FOXO4_(+)" "GABPB1_(+)" "GATA2_(+)"
## [100] "GATA3_(+)" "GATA5_(+)" "GATA6_(+)"
## [103] "GBX1_(+)" "GLI1_(+)" "GLIS2_(+)"
## [106] "GMEB1_(+)" "GMEB2_(+)" "GRHL1_(+)"
## [109] "GRHL2_(+)" "GRHPR_(+)" "GSC_(+)"
## [112] "GSC2_(+)" "GTF2B_(+)" "GTF2IRD1_(+)"
## [115] "GTF3A_(+)" "HAND1_(+)" "HDAC2_(+)"
## [118] "HES1_(+)" "HES5_(+)" "HES6_(+)"
## [121] "HESX1_(+)" "HEY2_(+)" "HINFP_(+)"
## [124] "HIVEP1_(+)" "HIVEP2_(+)" "HLF_(+)"
## [127] "HLX_(+)" "HMGB1_(+)" "HNF1A_(+)"
## [130] "HOXA2_(+)" "HOXA6_(+)" "HOXA9_(+)"
## [133] "HOXB4_(+)" "HOXB6_(+)" "HOXB7_(+)"
## [136] "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [139] "HOXC11_(+)" "HOXC13_(+)" "HOXC4_(+)"
## [142] "HOXC6_(+)" "HOXC8_(+)" "HOXD1_(+)"
## [145] "HOXD10_(+)" "HOXD4_(+)" "HOXD8_(+)"
## [148] "HOXD9_(+)" "HSF1_(+)" "HSF2_(+)"
## [151] "IKZF2_(+)" "ING3_(+)" "IRF1_(+)"
## [154] "IRF2_(+)" "IRF4_(+)" "IRF5_(+)"
## [157] "IRF6_(+)" "IRF7_(+)" "IRF8_(+)"
## [160] "IRF9_(+)" "IRX2_(+)" "ISL2_(+)"
## [163] "JUN_(+)" "JUND_(+)" "KDM4D_(+)"
## [166] "KDM5A_(+)" "KLF10_(+)" "KLF11_(+)"
## [169] "KLF12_(+)" "KLF13_(+)" "KLF14_(+)"
## [172] "KLF15_(+)" "KLF16_(+)" "KLF2_(+)"
## [175] "KLF5_(+)" "KLF6_(+)" "KLF7_(+)"
## [178] "KLF8_(+)" "KLF9_(+)" "LBX1_(+)"
## [181] "LHX1_(+)" "LHX4_(+)" "LHX5_(+)"
## [184] "LMX1B_(+)" "MAFA_(+)" "MAFB_(+)"
## [187] "MAFK_(+)" "MAX_(+)" "MAZ_(+)"
## [190] "MECOM_(+)" "MEF2C_(+)" "MEIS1_(+)"
## [193] "MEOX2_(+)" "MESP1_(+)" "MIOS_(+)"
## [196] "MITF_(+)" "MLXIP_(+)" "MLXIPL_(+)"
## [199] "MXI1_(+)" "MYBL1_(+)" "MYCN_(+)"
## [202] "MYEF2_(+)" "MYOD1_(+)" "MYPOP_(+)"
## [205] "MZF1_(+)" "NEUROD1_(+)" "NFATC2_(+)"
## [208] "NFE2_(+)" "NFE2L1_(+)" "NFE2L2_(+)"
## [211] "NFE2L3_(+)" "NFIC_(+)" "NFKB1_(+)"
## [214] "NFYA_(+)" "NFYC_(+)" "NHLH1_(+)"
## [217] "NHLH2_(+)" "NKX3-1_(+)" "NKX6-2_(+)"
## [220] "NPAS2_(+)" "NPDC1_(+)" "NR0B1_(+)"
## [223] "NR1H2_(+)" "NR1H3_(+)" "NR1H4_(+)"
## [226] "NR1I2_(+)" "NR2E1_(+)" "NR2F1_(+)"
## [229] "NR2F6_(+)" "NR4A1_(+)" "NR5A2_(+)"
## [232] "NRF1_(+)" "OLIG2_(+)" "OLIG3_(+)"
## [235] "ONECUT2_(+)" "OTP_(+)" "OVOL1_(+)"
## [238] "PAX7_(+)" "PAX8_(+)" "PAX9_(+)"
## [241] "PBX1_(+)" "PDX1_(+)" "PHF2_(+)"
## [244] "PHF21A_(+)" "PHF8_(+)" "PHOX2A_(+)"
## [247] "PKNOX1_(+)" "POLE3_(+)" "POLR2A_(+)"
## [250] "POLR3A_(+)" "POU2F1_(+)" "POU4F1_(+)"
## [253] "POU5F1_(+)" "POU5F1B_(+)" "POU6F1_(+)"
## [256] "PPARA_(+)" "PPARD_(+)" "PRDM1_(+)"
## [259] "PRDM16_(+)" "PRRX1_(+)" "PRRX2_(+)"
## [262] "RAD21_(+)" "RARA_(+)" "RARG_(+)"
## [265] "RBBP5_(+)" "REL_(+)" "RFX7_(+)"
## [268] "RREB1_(+)" "RUNX2_(+)" "SATB1_(+)"
## [271] "SETDB1_(+)" "SHOX2_(+)" "SIN3A_(+)"
## [274] "SIX1_(+)" "SIX2_(+)" "SIX5_(+)"
## [277] "SMAD1_(+)" "SMARCA5_(+)" "SMARCC2_(+)"
## [280] "SMC3_(+)" "SNAI3_(+)" "SNAPC4_(+)"
## [283] "SOX11_(+)" "SOX13_(+)" "SOX15_(+)"
## [286] "SOX2_(+)" "SOX21_(+)" "SOX4_(+)"
## [289] "SOX9_(+)" "SP1_(+)" "SP2_(+)"
## [292] "SP6_(+)" "SP7_(+)" "SP9_(+)"
## [295] "SPDEF_(+)" "SREBF2_(+)" "SRF_(+)"
## [298] "STAT1_(+)" "STAT2_(+)" "STAT4_(+)"
## [301] "STAT5B_(+)" "STAU2_(+)" "TAF7_(+)"
## [304] "TAL1_(+)" "TBP_(+)" "TBPL2_(+)"
## [307] "TBX15_(+)" "TBX18_(+)" "TBX20_(+)"
## [310] "TBX6_(+)" "TCF3_(+)" "TCF4_(+)"
## [313] "TCF7_(+)" "TCF7L1_(+)" "TEAD4_(+)"
## [316] "TET1_(+)" "TFAP2A_(+)" "TFAP2C_(+)"
## [319] "TFDP1_(+)" "TFDP2_(+)" "TFE3_(+)"
## [322] "TFEB_(+)" "TGIF2_(+)" "THAP1_(+)"
## [325] "TLX1_(+)" "TLX2_(+)" "TP73_(+)"
## [328] "TRIM28_(+)" "UBP1_(+)" "USF1_(+)"
## [331] "VAX1_(+)" "VAX2_(+)" "VDR_(+)"
## [334] "VEZF1_(+)" "VSX1_(+)" "VSX2_(+)"
## [337] "WT1_(+)" "YBX1_(+)" "YY2_(+)"
## [340] "ZBTB33_(+)" "ZEB1_(+)" "ZFHX2_(+)"
## [343] "ZFY_(+)" "ZNF134_(+)" "ZNF143_(+)"
## [346] "ZNF160_(+)" "ZNF208_(+)" "ZNF219_(+)"
## [349] "ZNF25_(+)" "ZNF264_(+)" "ZNF267_(+)"
## [352] "ZNF276_(+)" "ZNF316_(+)" "ZNF354C_(+)"
## [355] "ZNF384_(+)" "ZNF429_(+)" "ZNF441_(+)"
## [358] "ZNF471_(+)" "ZNF483_(+)" "ZNF486_(+)"
## [361] "ZNF513_(+)" "ZNF524_(+)" "ZNF550_(+)"
## [364] "ZNF554_(+)" "ZNF560_(+)" "ZNF606_(+)"
## [367] "ZNF607_(+)" "ZNF668_(+)" "ZNF672_(+)"
## [370] "ZNF713_(+)" "ZNF717_(+)" "ZNF721_(+)"
## [373] "ZNF761_(+)" "ZNF768_(+)" "ZNF787_(+)"
## [376] "ZNF8_(+)" "ZSCAN31_(+)" "ZXDC_(+)"
##
## $SARSCoV2_infected_NHBE
## [1] "AHCTF1_(+)" "AIRE_(+)" "ALX1_(+)" "ARID5B_(+)" "ARNT_(+)"
## [6] "ATF1_(+)" "BATF_(+)" "BBX_(+)" "BCL3_(+)" "BCL6B_(+)"
## [11] "CEBPB_(+)" "CEBPG_(+)" "CKMT1B_(+)" "CREB1_(+)" "CREB3_(+)"
## [16] "CREBL2_(+)" "DLX4_(+)" "DMRT1_(+)" "DMRTA1_(+)" "DUXA_(+)"
## [21] "EBF1_(+)" "EGR2_(+)" "ERF_(+)" "ESRRA_(+)" "ETV1_(+)"
## [26] "ETV6_(+)" "ETV7_(+)" "FOSL1_(+)" "FOXA2_(+)" "FOXF2_(+)"
## [31] "FOXK2_(+)" "FOXP3_(+)" "FOXQ1_(+)" "GATA2_(+)" "GATA3_(+)"
## [36] "HDAC2_(+)" "HES5_(+)" "HLF_(+)" "HNF1A_(+)" "HNF1B_(+)"
## [41] "HOXA2_(+)" "HOXA5_(+)" "HOXA7_(+)" "HOXA9_(+)" "HOXB5_(+)"
## [46] "HOXB6_(+)" "HOXB7_(+)" "HOXB8_(+)" "HOXB9_(+)" "HOXC10_(+)"
## [51] "HOXC4_(+)" "HOXC5_(+)" "HOXC6_(+)" "HOXC8_(+)" "HSF2_(+)"
## [56] "ING3_(+)" "IRF1_(+)" "IRF3_(+)" "IRF4_(+)" "IRF5_(+)"
## [61] "IRF8_(+)" "IRF9_(+)" "IRX2_(+)" "ISL2_(+)" "JUN_(+)"
## [66] "KLF10_(+)" "KLF5_(+)" "LHX1_(+)" "LHX4_(+)" "LHX8_(+)"
## [71] "LHX9_(+)" "MAFF_(+)" "MEOX2_(+)" "MIOS_(+)" "MLXIP_(+)"
## [76] "MSX1_(+)" "MSX2_(+)" "MXD4_(+)" "MYEF2_(+)" "NFIL3_(+)"
## [81] "NFYB_(+)" "NHLH1_(+)" "NKX2-1_(+)" "NKX3-1_(+)" "NR1I2_(+)"
## [86] "NR4A1_(+)" "NRF1_(+)" "ONECUT2_(+)" "OVOL2_(+)" "PAX2_(+)"
## [91] "PAX7_(+)" "PBX1_(+)" "PDX1_(+)" "PKNOX1_(+)" "POU2F3_(+)"
## [96] "PRDM16_(+)" "RARG_(+)" "RBBP5_(+)" "RELA_(+)" "RFX5_(+)"
## [101] "SIX2_(+)" "SMC3_(+)" "SOX13_(+)" "SOX2_(+)" "SP1_(+)"
## [106] "SP2_(+)" "SP4_(+)" "SP7_(+)" "SREBF2_(+)" "STAT1_(+)"
## [111] "STAT2_(+)" "TAF7_(+)" "TAGLN2_(+)" "TAL1_(+)" "TBP_(+)"
## [116] "TBPL1_(+)" "TBPL2_(+)" "TBX15_(+)" "TBX3_(+)" "TCF7_(+)"
## [121] "TET1_(+)" "TFAP2A_(+)" "TFE3_(+)" "TFEB_(+)" "TLX3_(+)"
## [126] "TWIST1_(+)" "UBTF_(+)" "UQCRB_(+)" "VSX1_(+)" "WT1_(+)"
## [131] "ZEB1_(+)" "ZFHX2_(+)" "ZFY_(+)" "ZNF160_(+)" "ZNF471_(+)"
## [136] "ZNF502_(+)" "ZNF560_(+)" "ZNF580_(+)" "ZNF768_(+)" "ZNF773_(+)"
## [141] "ZXDC_(+)"
##
## $human_IFNB_treated_NHBE
## [1] "ATF3_(+)" "BACH2_(+)" "ELF3_(+)" "ETV6_(+)" "ETV7_(+)"
## [6] "FOXA1_(+)" "FOXK1_(+)" "GATA2_(+)" "GCM1_(+)" "GTF2B_(+)"
## [11] "HIVEP2_(+)" "HLX_(+)" "HOXD11_(+)" "IRF1_(+)" "IRF2_(+)"
## [16] "IRF7_(+)" "IRF8_(+)" "IRF9_(+)" "NFIL3_(+)" "NFIX_(+)"
## [21] "NKX3-1_(+)" "POU5F1B_(+)" "PRDM16_(+)" "RARA_(+)" "RELA_(+)"
## [26] "RXRB_(+)" "SOX11_(+)" "SOX9_(+)" "STAT2_(+)" "TFEB_(+)"
## [31] "VEZF1_(+)"References
[1] https://www.cienciadedatos.net/documentos/19b_comparaciones_multiples_correccion_p-value_fdr
[2] https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html
sessionInfo()## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=es_MX.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=es_MX.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=es_MX.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] clusterProfiler_4.0.5 ggrepel_0.9.1 enrichplot_1.12.3
## [4] ggpubr_0.4.0.999 org.Hs.eg.db_3.13.0 AnnotationDbi_1.54.1
## [7] IRanges_2.26.0 S4Vectors_0.30.2 Biobase_2.52.0
## [10] BiocGenerics_0.38.0 RColorBrewer_1.1-2 circlize_0.4.14
## [13] ComplexHeatmap_2.8.0 forcats_0.5.1 stringr_1.4.0
## [16] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
## [19] tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.5
## [22] tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] shadowtext_0.1.1 readxl_1.4.0 backports_1.4.1
## [4] fastmatch_1.1-3 plyr_1.8.7 igraph_1.2.11
## [7] lazyeval_0.2.2 splines_4.1.1 BiocParallel_1.26.2
## [10] GenomeInfoDb_1.28.4 digest_0.6.29 yulab.utils_0.0.4
## [13] foreach_1.5.2 htmltools_0.5.2 GOSemSim_2.18.1
## [16] viridis_0.6.2 GO.db_3.13.0 fansi_1.0.3
## [19] magrittr_2.0.3 memoise_2.0.1 cluster_2.1.2
## [22] doParallel_1.0.17 tzdb_0.3.0 Biostrings_2.60.2
## [25] graphlayouts_0.8.0 modelr_0.1.8 matrixStats_0.61.0
## [28] vroom_1.5.7 colorspace_2.0-3 blob_1.2.2
## [31] rvest_1.0.2 haven_2.4.3 xfun_0.31
## [34] crayon_1.5.1 RCurl_1.98-1.6 jsonlite_1.8.0
## [37] scatterpie_0.1.7 ape_5.6-2 iterators_1.0.14
## [40] glue_1.6.2 polyclip_1.10-0 gtable_0.3.0
## [43] zlibbioc_1.38.0 XVector_0.32.0 GetoptLong_1.0.5
## [46] car_3.0-12 shape_1.4.6 abind_1.4-5
## [49] scales_1.1.1 DOSE_3.18.3 DBI_1.1.2
## [52] rstatix_0.7.0 Rcpp_1.0.8.3 viridisLite_0.4.0
## [55] clue_0.3-60 tidytree_0.3.9 gridGraphics_0.5-1
## [58] bit_4.0.4 httr_1.4.3 fgsea_1.18.0
## [61] ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0
## [64] sass_0.4.1 dbplyr_2.1.1 utf8_1.2.2
## [67] labeling_0.4.2 ggplotify_0.1.0 tidyselect_1.1.2
## [70] rlang_1.0.2 reshape2_1.4.4 munsell_0.5.0
## [73] cellranger_1.1.0 tools_4.1.1 cachem_1.0.6
## [76] downloader_0.4 cli_3.3.0 generics_0.1.2
## [79] RSQLite_2.2.11 broom_0.7.12 evaluate_0.15
## [82] fastmap_1.1.0 yaml_2.3.5 ggtree_3.0.4
## [85] knitr_1.39 bit64_4.0.5 fs_1.5.2
## [88] tidygraph_1.2.0 KEGGREST_1.32.0 ggraph_2.0.5
## [91] nlme_3.1-152 aplot_0.1.2 DO.db_2.9
## [94] xml2_1.3.3 compiler_4.1.1 rstudioapi_0.13
## [97] png_0.1-7 ggsignif_0.6.3 treeio_1.16.2
## [100] reprex_2.0.1 tweenr_1.0.2 bslib_0.3.1
## [103] stringi_1.7.6 highr_0.9 lattice_0.20-44
## [106] Matrix_1.3-4 vctrs_0.4.1 pillar_1.7.0
## [109] lifecycle_1.0.1 jquerylib_0.1.4 GlobalOptions_0.1.2
## [112] cowplot_1.1.1 data.table_1.14.2 bitops_1.0-7
## [115] patchwork_1.1.1 qvalue_2.24.0 R6_2.5.1
## [118] gridExtra_2.3 codetools_0.2-18 MASS_7.3-54
## [121] assertthat_0.2.1 rjson_0.2.21 withr_2.5.0
## [124] GenomeInfoDbData_1.2.6 hms_1.1.1 ggfun_0.0.5
## [127] rmarkdown_2.14 carData_3.0-5 Cairo_1.5-15
## [130] ggforce_0.3.3 lubridate_1.8.0